From 21ecd68bfe415ee78173813667f1bb0d465f7f4b Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 27 Jan 2022 08:43:02 +0100
Subject: [PATCH 01/83] fix: remove left-over unnecessary code

---
 modules/deeparg/predict/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/deeparg/predict/main.nf b/modules/deeparg/predict/main.nf
index 1af0fd40..9408fa3d 100644
--- a/modules/deeparg/predict/main.nf
+++ b/modules/deeparg/predict/main.nf
@@ -11,7 +11,7 @@ process DEEPARG_PREDICT {
 
     input:
     tuple val(meta), path(fasta), val(model)
-    tuple path(db)
+    path(db)
 
     output:
     tuple val(meta), path("*.align.daa")            , emit: daa

From 0f7c04647747f535c94f63908bdd82c77f9a9ed1 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 13 Apr 2022 12:51:17 +0200
Subject: [PATCH 02/83] first commit

---
 modules/elprep/merge/main.nf               | 44 ++++++++++++++++++++++
 modules/elprep/merge/meta.yml              | 44 ++++++++++++++++++++++
 tests/config/pytest_modules.yml            |  4 ++
 tests/modules/elprep/merge/main.nf         | 17 +++++++++
 tests/modules/elprep/merge/nextflow.config |  5 +++
 tests/modules/elprep/merge/test.yml        | 11 ++++++
 6 files changed, 125 insertions(+)
 create mode 100644 modules/elprep/merge/main.nf
 create mode 100644 modules/elprep/merge/meta.yml
 create mode 100644 tests/modules/elprep/merge/main.nf
 create mode 100644 tests/modules/elprep/merge/nextflow.config
 create mode 100644 tests/modules/elprep/merge/test.yml

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
new file mode 100644
index 00000000..8312d35b
--- /dev/null
+++ b/modules/elprep/merge/main.nf
@@ -0,0 +1,44 @@
+process ELPREP_MERGE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
+        'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("**.{bam,sam}"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        args += " --single-end"
+    }
+    def suffix = args.contains("--output-type sam") ? "sam" : "bam"
+
+    """
+    # create directory and move all input so elprep can find and merge them before splitting
+    mkdir input
+    mv ${bam} input/
+
+    elprep merge \\
+        input \\
+        ${prefix}.${suffix} \\
+        $args \\
+        --nr-of-threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/elprep/merge/meta.yml b/modules/elprep/merge/meta.yml
new file mode 100644
index 00000000..e157fddb
--- /dev/null
+++ b/modules/elprep/merge/meta.yml
@@ -0,0 +1,44 @@
+name: "elprep_merge"
+description: Merge split bam/sam chunks in one file
+keywords:
+  - bam
+  - sam
+  - merge
+tools:
+  - "elprep":
+      description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      doi: ""
+      licence: "['AGPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: List of BAM/SAM chunks to merge
+      pattern: "*.{bam,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  #
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - bam:
+      type: file
+      description: Merged BAM/SAM file
+      pattern: "*.{bam,sam}"
+
+authors:
+  - "@matthdsm"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index cd4913cf..ea22a0d6 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -587,6 +587,10 @@ ectyper:
   - modules/ectyper/**
   - tests/modules/ectyper/**
 
+elprep/merge:
+  - modules/elprep/merge/**
+  - tests/modules/elprep/merge/**
+
 emmtyper:
   - modules/emmtyper/**
   - tests/modules/emmtyper/**
diff --git a/tests/modules/elprep/merge/main.nf b/tests/modules/elprep/merge/main.nf
new file mode 100644
index 00000000..b4a40ce3
--- /dev/null
+++ b/tests/modules/elprep/merge/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
+include { ELPREP_MERGE } from '../../../../modules/elprep/merge/main.nf'
+
+workflow test_elprep_merge {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    ELPREP_SPLIT ( input )
+    ELPREP_MERGE ( ELPREP_SPLIT.out.bam )
+}
diff --git a/tests/modules/elprep/merge/nextflow.config b/tests/modules/elprep/merge/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/elprep/merge/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
new file mode 100644
index 00000000..c66fe030
--- /dev/null
+++ b/tests/modules/elprep/merge/test.yml
@@ -0,0 +1,11 @@
+- name: "elprep merge"
+  command: nextflow run ./tests/modules/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config -c ./tests/modules/elprep/merge/nextflow.config
+  tags:
+    - "elprep"
+    #
+    - "elprep/merge"
+    #
+  files:
+    - path: "output/elprep/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/elprep/versions.yml

From ccef7f857917189fe1c2563c4d68deb038bade4b Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 11:26:01 +0200
Subject: [PATCH 03/83] alignment

---
 modules/elprep/merge/main.nf        | 4 ++--
 tests/modules/elprep/merge/test.yml | 3 ---
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 8312d35b..010156f2 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -11,8 +11,8 @@ process ELPREP_MERGE {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("**.{bam,sam}"), emit: bam
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("**.{bam,sam}")   , emit: bam
+    path "versions.yml"                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
index c66fe030..26c16f59 100644
--- a/tests/modules/elprep/merge/test.yml
+++ b/tests/modules/elprep/merge/test.yml
@@ -2,10 +2,7 @@
   command: nextflow run ./tests/modules/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config -c ./tests/modules/elprep/merge/nextflow.config
   tags:
     - "elprep"
-    #
     - "elprep/merge"
-    #
   files:
     - path: "output/elprep/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
     - path: output/elprep/versions.yml

From ad15d1b7922c8de1b4b84897e4a44182f5b52299 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 11:27:55 +0200
Subject: [PATCH 04/83] update label

---
 modules/elprep/merge/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 010156f2..00ed4d60 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -1,6 +1,6 @@
 process ELPREP_MERGE {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
 
     conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

From 6723ca7f9068ecbdee31dcad07f3115dc5b40667 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:05:02 +0200
Subject: [PATCH 05/83] bump version, add merge before split

---
 modules/bamtools/split/main.nf  | 22 +++++++++++++++-------
 modules/bamtools/split/meta.yml |  8 +++++++-
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 014e5cdb..f6382d97 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -2,13 +2,14 @@ process BAMTOOLS_SPLIT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
-        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
+        'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
 
     input:
     tuple val(meta), path(bam)
+    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -19,12 +20,19 @@ process BAMTOOLS_SPLIT {
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_list = bam.collect{"-in $it"}.join(' ')
+    if (bam_list) {
+        input += " -list $bam_list"
+    }
+
     """
-    bamtools \\
-        split \\
-        -in $bam \\
-        $args
+    bamtools merge \\
+        ${input_list} \\
+        $args \\
+    bamtools split \\
+        $args2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index 0e848212..6c534281 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -23,8 +23,13 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: A BAM file to split
+      description: A list of BAM files to merge and then split
       pattern: "*.bam"
+  - bam_list:
+      type: file
+      description: |
+        Input file containing bam files to merge before splitting,
+        one line per file
 
 output:
   - meta:
@@ -43,3 +48,4 @@ output:
 
 authors:
   - "@sguizard"
+  - "@matthdsm"

From b35264e9196d8f7c74c28a7bd5bc126a5e16afe8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:11:37 +0200
Subject: [PATCH 06/83] bugfixes

---
 modules/bamtools/split/main.nf       | 6 ++----
 modules/bamtools/split/meta.yml      | 2 +-
 tests/modules/bamtools/split/main.nf | 2 +-
 3 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index f6382d97..2f5ef09f 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -20,7 +20,6 @@ process BAMTOOLS_SPLIT {
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
     if (bam_list) {
@@ -30,9 +29,8 @@ process BAMTOOLS_SPLIT {
     """
     bamtools merge \\
         ${input_list} \\
-        $args \\
-    bamtools split \\
-        $args2
+    | bamtools split \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index 6c534281..0fd5d5ca 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -28,7 +28,7 @@ input:
   - bam_list:
       type: file
       description: |
-        Input file containing bam files to merge before splitting,
+        Optional input file containing bam files to merge before splitting,
         one line per file
 
 output:
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index eb0bed01..9f30c4f9 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -10,5 +10,5 @@ workflow test_bamtools_split {
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT ( input, [] )
 }

From 07982d6cb13649c308625bb3d215c39979e1207c Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Tue, 19 Apr 2022 15:31:39 +0200
Subject: [PATCH 07/83] fix command line, fix meta.yml

---
 modules/bamtools/split/main.nf        | 5 ++++-
 tests/modules/bamtools/split/test.yml | 9 +++++----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 2f5ef09f..f72d13be 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -23,7 +23,10 @@ process BAMTOOLS_SPLIT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
     if (bam_list) {
-        input += " -list $bam_list"
+        input_list += " -list $bam_list"
+    }
+    if (!args.contains("-stub")) {
+        args += " -stub ${prefix}"
     }
 
     """
diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index 4f52e9ce..b52cc9ee 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,10 +1,11 @@
 - name: bamtools split test_bamtools_split
-  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
+  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config
   tags:
-    - bamtools/split
     - bamtools
+    - bamtools/split
   files:
-    - path: output/bamtools/test.paired_end.sorted.REF_chr22.bam
+    - path: output/bamtools/test.REF_chr22.bam
       md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
-    - path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam
+    - path: output/bamtools/test.REF_unmapped.bam
       md5sum: e0754bf72c51543b2d745d96537035fb
+    - path: output/bamtools/versions.yml

From d85f9c7011a2539dc07582c1642f4255a3724b7c Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 21 Apr 2022 13:16:23 +0200
Subject: [PATCH 08/83] add subworkflow bam_qc_picard

---
 subworkflows/nf-core/bam_qc_picard/main.nf    | 43 +++++++++++++
 subworkflows/nf-core/bam_qc_picard/meta.yml   | 64 +++++++++++++++++++
 .../nf-core/bam_qc_picard/main.nf             | 21 ++++++
 .../nf-core/bam_qc_picard/test.yml            | 33 ++++++++++
 4 files changed, 161 insertions(+)
 create mode 100644 subworkflows/nf-core/bam_qc_picard/main.nf
 create mode 100644 subworkflows/nf-core/bam_qc_picard/meta.yml
 create mode 100644 tests/subworkflows/nf-core/bam_qc_picard/main.nf
 create mode 100644 tests/subworkflows/nf-core/bam_qc_picard/test.yml

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
new file mode 100644
index 00000000..31edb2c3
--- /dev/null
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -0,0 +1,43 @@
+//
+// Run QC steps on BAM/CRAM files using Picard
+//
+
+params.options = [:]
+
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picardcollectmultiplemetrics/main' addParams( options: params.options )
+include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picardcollectwgsmetrics/main'      addParams( options: params.options )
+include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picardcollecthsmetrics/main'       addParams( options: params.options )
+
+workflow BAM_QC_PICARD {
+    take:
+    ch_bam_bai          // channel: [ val(meta), [ bam ], [bai/csi] ]
+    ch_fasta            // channel: [ fasta ]
+    ch_bait_interval    // channel: [ bait_interval ]
+    ch_target_interval  // channel: [ target_interval ]
+
+    main:
+    ch_versions = Channel.empty()
+
+    PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta] )
+    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+    if (!ch_bait_interval.isEmpty() || !ch_target_interval.isEmpty()) {
+        if (ch_bait_interval.isEmpty()) {
+            throw new Error("Bait interval channel is empty")
+        }
+        if (ch_target_interval.isEmpty()) {
+            throw new Error("Target interval channel is empty")
+        }
+        PICARD_COLLECTHSMETRICS( ch_bam_bai, ch_fasta, ch_bait_interval, ch_target_interval )
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+    } else {
+        PICARD_COLLECTWGSMETRICS( ch_bam_bai, ch_fasta )
+        ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
+    }
+
+    emit:
+    hs_metrics          = PICARD_COLLECTHSMETRICS.out.hs_metrics    // channel: [ val(meta), [ hs_metrics ] ]
+    wgs_metrics         = PICARD_COLLECTWGSMETRICS.out.metrics      // channel: [ val(meta), [ wgs_metrics ] ]
+    multiple_metrics    = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
+
+    versions = ch_versions                                          // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
new file mode 100644
index 00000000..77104e82
--- /dev/null
+++ b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -0,0 +1,64 @@
+name: bam_qc
+description: Produces comprehensive statistics from BAM file
+keywords:
+  - statistics
+  - counts
+  - hs_metrics
+  - wgs_metrics
+  - bam
+  - sam
+  - cram
+modules:
+  - picard/collectmultiplemetrics
+  - picard/collectwgsmetrics
+  - picard/collecthsmetrics
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: Index for BAM/CRAM/SAM file
+      pattern: "*.{bai,crai,sai}"
+  - fasta:
+      type: optional file
+      description: Reference file the CRAM was created with
+      pattern: "*.{fasta,fa}"
+  - bait_intervals:
+      type: optional file
+      description: An interval list file that contains the locations of the baits used.
+      pattern: "baits.interval_list"
+  - target_intervals:
+      type: optional file
+      description: An interval list file that contains the locations of the targets.
+      pattern: "targets.interval_list"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - hs_metrics:
+      type: file
+      description: Alignment metrics files generated by picard CollectHsMetrics
+      pattern: "*_collecthsmetrics.txt"
+  - wgs_metrics:
+      type: file
+      description: Alignment metrics files generated by picard CollectWgsMetrics
+      pattern: "*_{metrics}"
+  - multiple_metrics:
+      type: file
+      description: Alignment metrics files generated by picard CollectMultipleMetrics
+      pattern: "*_{metrics}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@matthdsm"
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/main.nf b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
new file mode 100644
index 00000000..d88f2bf9
--- /dev/null
+++ b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/main' addParams([:])
+
+workflow test_bam_qc_picard_wgs {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+            ]
+
+    BAM_QC_PICARD ( input, [], [], [] )
+}
+
+workflow test_bam_qc_picard_targetted {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    BAM_QC_PICARD ( input, [], file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true) )
+}
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/test.yml b/tests/subworkflows/nf-core/bam_qc_picard/test.yml
new file mode 100644
index 00000000..af98230d
--- /dev/null
+++ b/tests/subworkflows/nf-core/bam_qc_picard/test.yml
@@ -0,0 +1,33 @@
+- name: bam qc picard wgs
+  command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_wgs -c tests/config/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/bam_qc_picard
+    # Modules
+    # - picard
+    # - picard/collectmultiplemetrics
+    # - picard/collectwgsmetrics
+  files:
+    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: ./output/picard/test.CollectWgsMetrics.coverage_metrics
+
+- name: bam qc picard targetted
+  command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_targetted -c tests/config/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/bam_qc_picard
+    # Modules
+    # - picard
+    # - picard/collectmultiplemetrics
+    # - picard/collecthsmetrics
+  files:
+    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: ./output/picard/test_collecthsmetrics.txt

From 8dad38afc7f28db49c38a23deb7abfeca2ee3bc7 Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 11:35:14 +0200
Subject: [PATCH 09/83] fix test.yml

---
 tests/modules/elprep/merge/test.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
index 26c16f59..d6037bec 100644
--- a/tests/modules/elprep/merge/test.yml
+++ b/tests/modules/elprep/merge/test.yml
@@ -1,8 +1,8 @@
-- name: "elprep merge"
-  command: nextflow run ./tests/modules/elprep/merge -entry test_elprep_merge -c ./tests/config/nextflow.config -c ./tests/modules/elprep/merge/nextflow.config
+- name: elprep merge test_elprep_merge
+  command: nextflow run tests/modules/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config
   tags:
-    - "elprep"
-    - "elprep/merge"
+    - elprep
+    - elprep/merge
   files:
-    - path: "output/elprep/test.bam"
+    - path: output/elprep/test.bam
     - path: output/elprep/versions.yml

From c4072f274cdf91601c895b206f2011e0b4b809df Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:39:22 +0200
Subject: [PATCH 10/83] fix formatting, fix code style

---
 modules/elprep/merge/main.nf | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 00ed4d60..2b12bfe2 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -18,12 +18,10 @@ process ELPREP_MERGE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        args += " --single-end"
-    }
-    def suffix = args.contains("--output-type sam") ? "sam" : "bam"
+    def args        = task.ext.args ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def suffix      = args.contains("--output-type sam") ? "sam" : "bam"
+    def single_end  = meta.single_end ? " --single-end" : ""
 
     """
     # create directory and move all input so elprep can find and merge them before splitting
@@ -34,6 +32,7 @@ process ELPREP_MERGE {
         input \\
         ${prefix}.${suffix} \\
         $args \\
+        ${single_end} \\
         --nr-of-threads $task.cpus
 
     cat <<-END_VERSIONS > versions.yml

From 2f6382168cac2ca8a9ff9d53c868fbde1a0ca5e1 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 11:51:54 +0200
Subject: [PATCH 11/83] update meta.yml

---
 modules/elprep/merge/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/elprep/merge/meta.yml b/modules/elprep/merge/meta.yml
index e157fddb..1f49b1a0 100644
--- a/modules/elprep/merge/meta.yml
+++ b/modules/elprep/merge/meta.yml
@@ -7,10 +7,10 @@ keywords:
 tools:
   - "elprep":
       description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
-      homepage: "None"
-      documentation: "None"
-      tool_dev_url: "None"
-      doi: ""
+      homepage: "https://github.com/ExaScience/elprep"
+      documentation: "https://github.com/ExaScience/elprep"
+      tool_dev_url: "https://github.com/ExaScience/elprep"
+      doi: "10.1371/journal.pone.0244471"
       licence: "['AGPL v3']"
 
 input:

From fefffb9bb0776e679c2297e8d80325d57e2f2d7a Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 12:36:32 +0200
Subject: [PATCH 12/83] fix output glob

---
 modules/elprep/merge/main.nf        | 6 +++---
 tests/modules/elprep/merge/test.yml | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 2b12bfe2..28fa9985 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -11,8 +11,8 @@ process ELPREP_MERGE {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("**.{bam,sam}")   , emit: bam
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("output/**.{bam,sam}")    , emit: bam
+    path "versions.yml"                             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,7 +30,7 @@ process ELPREP_MERGE {
 
     elprep merge \\
         input \\
-        ${prefix}.${suffix} \\
+        output/${prefix}.${suffix} \\
         $args \\
         ${single_end} \\
         --nr-of-threads $task.cpus
diff --git a/tests/modules/elprep/merge/test.yml b/tests/modules/elprep/merge/test.yml
index d6037bec..ad2ecfef 100644
--- a/tests/modules/elprep/merge/test.yml
+++ b/tests/modules/elprep/merge/test.yml
@@ -4,5 +4,5 @@
     - elprep
     - elprep/merge
   files:
-    - path: output/elprep/test.bam
+    - path: output/elprep/output/test.bam
     - path: output/elprep/versions.yml

From 9a2dad935cad22789380f94b67a44181e89e4392 Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 13:13:39 +0200
Subject: [PATCH 13/83] update config

---
 tests/modules/elprep/merge/nextflow.config | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/modules/elprep/merge/nextflow.config b/tests/modules/elprep/merge/nextflow.config
index 50f50a7a..4e4570f4 100644
--- a/tests/modules/elprep/merge/nextflow.config
+++ b/tests/modules/elprep/merge/nextflow.config
@@ -1,5 +1,5 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
+    withName : ELPREP_MERGE {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+}

From 413980e93a9cb8ba51f430d8a794cb25c43e9305 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:33:16 +0200
Subject: [PATCH 14/83] make use of  dependent on input array size

---
 modules/bamtools/split/main.nf | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index f72d13be..7d69a824 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -9,7 +9,6 @@ process BAMTOOLS_SPLIT {
 
     input:
     tuple val(meta), path(bam)
-    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -21,18 +20,22 @@ process BAMTOOLS_SPLIT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
     def input_list = bam.collect{"-in $it"}.join(' ')
-    if (bam_list) {
-        input_list += " -list $bam_list"
-    }
-    if (!args.contains("-stub")) {
-        args += " -stub ${prefix}"
+    def stub_cmd = !args.contains("-stub") : " -stub ${prefix}" : ""
+
+    if (size(bam) > 1){
+        def bamtools_merge_cmd = "bamtools merge ${input_list} |"
+    } else {
+        def split_input = input_list
     }
 
+
     """
-    bamtools merge \\
-        ${input_list} \\
-    | bamtools split \\
+    ${bamtools_merge_cmd} \\
+    bamtools split \\
+        $split_input \\
+        $stub_cmd \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

From d617a50371abf87bdb376844926088c478ae3f51 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:39:25 +0200
Subject: [PATCH 15/83] add extra test

---
 tests/modules/bamtools/split/main.nf | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index 9f30c4f9..2fc16d67 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -4,11 +4,21 @@ nextflow.enable.dsl = 2
 
 include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
 
-workflow test_bamtools_split {
+workflow test_bamtools_split_single_input {
 
     input = [
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
 
-    BAMTOOLS_SPLIT ( input, [] )
+    BAMTOOLS_SPLIT ( input )
+}
+
+workflow test_bamtools_split_multiple_input {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
+    [
+
+    BAMTOOLS_SPLIT ( input )
 }

From d293cffc6a3beb7f1ef9bab6e95ea421f622b2a5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:42:43 +0200
Subject: [PATCH 16/83] update tests

---
 tests/modules/bamtools/split/main.nf | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index 2fc16d67..ef4b9d59 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -2,15 +2,17 @@
 
 nextflow.enable.dsl = 2
 
-include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE   } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/bamtools/split/main.nf'
 
 workflow test_bamtools_split_single_input {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT_SINGLE ( input )
 }
 
 workflow test_bamtools_split_multiple_input {
@@ -20,5 +22,5 @@ workflow test_bamtools_split_multiple_input {
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
     [
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT_MULTIPLE ( input )
 }

From 7e883da90460f77b3745468452b4c549327dde13 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 14:50:50 +0200
Subject: [PATCH 17/83] Revert "make use of  dependent on input array size"

This reverts commit 413980e93a9cb8ba51f430d8a794cb25c43e9305.
---
 modules/bamtools/split/main.nf | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 7d69a824..f72d13be 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -9,6 +9,7 @@ process BAMTOOLS_SPLIT {
 
     input:
     tuple val(meta), path(bam)
+    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -20,22 +21,18 @@ process BAMTOOLS_SPLIT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     def input_list = bam.collect{"-in $it"}.join(' ')
-    def stub_cmd = !args.contains("-stub") : " -stub ${prefix}" : ""
-
-    if (size(bam) > 1){
-        def bamtools_merge_cmd = "bamtools merge ${input_list} |"
-    } else {
-        def split_input = input_list
+    if (bam_list) {
+        input_list += " -list $bam_list"
+    }
+    if (!args.contains("-stub")) {
+        args += " -stub ${prefix}"
     }
 
-
     """
-    ${bamtools_merge_cmd} \\
-    bamtools split \\
-        $split_input \\
-        $stub_cmd \\
+    bamtools merge \\
+        ${input_list} \\
+    | bamtools split \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

From b4af3f1475b91d0c411e901d6126515babcdafec Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 15:02:41 +0200
Subject: [PATCH 18/83] test fixes

---
 modules/bamtools/split/main.nf       | 9 ++-------
 tests/modules/bamtools/split/main.nf | 9 ++++++---
 2 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index f72d13be..7184261e 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -9,7 +9,6 @@ process BAMTOOLS_SPLIT {
 
     input:
     tuple val(meta), path(bam)
-    path(bam_list)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -22,17 +21,13 @@ process BAMTOOLS_SPLIT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
-    if (bam_list) {
-        input_list += " -list $bam_list"
-    }
-    if (!args.contains("-stub")) {
-        args += " -stub ${prefix}"
-    }
+    def stub =  !args.contains("-stub") ? "-stub ${prefix}" : ""
 
     """
     bamtools merge \\
         ${input_list} \\
     | bamtools split \\
+        $stub \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index ef4b9d59..ff0cb748 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -15,12 +15,15 @@ workflow test_bamtools_split_single_input {
     BAMTOOLS_SPLIT_SINGLE ( input )
 }
 
-workflow test_bamtools_split_multiple_input {
+workflow test_bamtools_split_multiple {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
-    [
+        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]
+
+    ]
 
     BAMTOOLS_SPLIT_MULTIPLE ( input )
 }
+

From 3bcae8e71e705f289ec3786e7b6255eb5e0d56af Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 22 Apr 2022 15:19:52 +0200
Subject: [PATCH 19/83] fix testing errors

---
 tests/modules/bamtools/split/main.nf  |  2 +-
 tests/modules/bamtools/split/test.yml | 16 ++++++++++++++--
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index ff0cb748..9787b4ed 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -20,7 +20,7 @@ workflow test_bamtools_split_multiple {
     input = [
         [ id:'test', single_end:false ], // meta map
         [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
 
     ]
 
diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index b52cc9ee..63ecac57 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,5 +1,5 @@
-- name: bamtools split test_bamtools_split
-  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split -c tests/config/nextflow.config
+- name: bamtools split test_bamtools_split_single_input
+  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_single_input -c tests/config/nextflow.config
   tags:
     - bamtools
     - bamtools/split
@@ -9,3 +9,15 @@
     - path: output/bamtools/test.REF_unmapped.bam
       md5sum: e0754bf72c51543b2d745d96537035fb
     - path: output/bamtools/versions.yml
+
+- name: bamtools split test_bamtools_split_multiple
+  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_multiple -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/split
+  files:
+    - path: output/bamtools/test.REF_chr22.bam
+      md5sum: 585675bea34c48ebe9db06a561d4b4fa
+    - path: output/bamtools/test.REF_unmapped.bam
+      md5sum: 16ad644c87b9471f3026bc87c98b4963
+    - path: output/bamtools/versions.yml

From 2a2ac290c37fbbd6caa41b06993818491131e0f2 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:00 +0200
Subject: [PATCH 20/83] Update modules/bamtools/split/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index 0fd5d5ca..badc6974 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -23,7 +23,7 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: A list of BAM files to merge and then split
+      description: A list of one or more BAM files to merge and then split
       pattern: "*.bam"
   - bam_list:
       type: file

From 7bcede747411d77f85dde0c33e3599e81c0cdb14 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:14 +0200
Subject: [PATCH 21/83] Update modules/bamtools/split/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/meta.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml
index badc6974..8af701f0 100644
--- a/modules/bamtools/split/meta.yml
+++ b/modules/bamtools/split/meta.yml
@@ -25,11 +25,6 @@ input:
       type: file
       description: A list of one or more BAM files to merge and then split
       pattern: "*.bam"
-  - bam_list:
-      type: file
-      description: |
-        Optional input file containing bam files to merge before splitting,
-        one line per file
 
 output:
   - meta:

From b73662c8d9b5a770904ae9f3b1a79c878f125c6c Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:32 +0200
Subject: [PATCH 22/83] Update tests/modules/bamtools/split/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bamtools/split/main.nf | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/modules/bamtools/split/main.nf b/tests/modules/bamtools/split/main.nf
index 9787b4ed..e5c15c32 100644
--- a/tests/modules/bamtools/split/main.nf
+++ b/tests/modules/bamtools/split/main.nf
@@ -19,9 +19,10 @@ workflow test_bamtools_split_multiple {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
-
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+        ]
     ]
 
     BAMTOOLS_SPLIT_MULTIPLE ( input )

From 6efb022f6943ff67421b46359b38582a36278fe5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:34:44 +0200
Subject: [PATCH 23/83] Update tests/modules/bamtools/split/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bamtools/split/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index 63ecac57..5747aa25 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -11,7 +11,7 @@
     - path: output/bamtools/versions.yml
 
 - name: bamtools split test_bamtools_split_multiple
-  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_multiple -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
   tags:
     - bamtools
     - bamtools/split

From e9c44f3d85b731add02680fa6a246c0675e1aac7 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:35:34 +0200
Subject: [PATCH 24/83] Update tests/modules/bamtools/split/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/modules/bamtools/split/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/bamtools/split/test.yml b/tests/modules/bamtools/split/test.yml
index 5747aa25..af639b43 100644
--- a/tests/modules/bamtools/split/test.yml
+++ b/tests/modules/bamtools/split/test.yml
@@ -1,5 +1,5 @@
 - name: bamtools split test_bamtools_split_single_input
-  command: nextflow run tests/modules/bamtools/split -entry test_bamtools_split_single_input -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
   tags:
     - bamtools
     - bamtools/split

From 2d32267fcdce945375294cb776ca129038d2b903 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:36:01 +0200
Subject: [PATCH 25/83] Update modules/bamtools/split/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/main.nf | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 7184261e..9c643b84 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -24,11 +24,13 @@ process BAMTOOLS_SPLIT {
     def stub =  !args.contains("-stub") ? "-stub ${prefix}" : ""
 
     """
-    bamtools merge \\
-        ${input_list} \\
-    | bamtools split \\
-        $stub \\
-        $args
+    bamtools \\
+        merge \\
+        $input_list \\
+        | bamtools \\
+            split \\
+            -stub $prefix \\
+            $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From da56a2d50968f12ff2aa1a6d6b05fae083ba26c3 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 22 Apr 2022 19:36:08 +0200
Subject: [PATCH 26/83] Update modules/bamtools/split/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/bamtools/split/main.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/bamtools/split/main.nf b/modules/bamtools/split/main.nf
index 9c643b84..aaa5b663 100644
--- a/modules/bamtools/split/main.nf
+++ b/modules/bamtools/split/main.nf
@@ -21,8 +21,6 @@ process BAMTOOLS_SPLIT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"-in $it"}.join(' ')
-    def stub =  !args.contains("-stub") ? "-stub ${prefix}" : ""
-
     """
     bamtools \\
         merge \\

From 569e07f0af74e2a6ea43fca61ae90bb762893461 Mon Sep 17 00:00:00 2001
From: "Maxime U. Garcia" <maxime.garcia@scilifelab.se>
Date: Mon, 25 Apr 2022 14:32:49 +0200
Subject: [PATCH 27/83] add samtools/bamtocram modules (#1561)

* add new samtools/bamtocram module

* fix md5sum

* remove md5sum

* Update modules/samtools/bamtocram/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/samtools/bamtocram/main.nf            | 35 +++++++++++++
 modules/samtools/bamtocram/meta.yml           | 52 +++++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/modules/samtools/bamtocram/main.nf      | 17 ++++++
 .../samtools/bamtocram/nextflow.config        |  5 ++
 tests/modules/samtools/bamtocram/test.yml     |  9 ++++
 6 files changed, 122 insertions(+)
 create mode 100644 modules/samtools/bamtocram/main.nf
 create mode 100644 modules/samtools/bamtocram/meta.yml
 create mode 100644 tests/modules/samtools/bamtocram/main.nf
 create mode 100644 tests/modules/samtools/bamtocram/nextflow.config
 create mode 100644 tests/modules/samtools/bamtocram/test.yml

diff --git a/modules/samtools/bamtocram/main.nf b/modules/samtools/bamtocram/main.nf
new file mode 100644
index 00000000..b49c308f
--- /dev/null
+++ b/modules/samtools/bamtocram/main.nf
@@ -0,0 +1,35 @@
+//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
+process SAMTOOLS_BAMTOCRAM {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(input), path(index)
+    path  fasta
+    path  fai
+
+    output:
+    tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
+    path  "versions.yml"                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args  ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
+    samtools index -@${task.cpus} ${prefix}.cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/samtools/bamtocram/meta.yml b/modules/samtools/bamtocram/meta.yml
new file mode 100644
index 00000000..037704c6
--- /dev/null
+++ b/modules/samtools/bamtocram/meta.yml
@@ -0,0 +1,52 @@
+name: samtools_bamtocram
+description: filter/convert and then index CRAM file
+keywords:
+  - view
+  - index
+  - bam
+  - cram
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/SAM file
+      pattern: "*.{bam,sam}"
+  - index:
+      type: file
+      description: BAM/SAM index file
+      pattern: "*.{bai,sai}"
+  - fasta:
+      type: file
+      description: Reference file to create the CRAM file
+      pattern: "*.{fasta,fa}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cram_crai:
+      type: file
+      description: filtered/converted CRAM file + index
+      pattern: "*{.cram,.crai}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@FriederikeHanssen"
+  - "@maxulysse"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 263e83a8..4d8ce0b5 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1595,6 +1595,10 @@ samtools/bam2fq:
   - modules/samtools/bam2fq/**
   - tests/modules/samtools/bam2fq/**
 
+samtools/bamtocram:
+  - modules/samtools/bamtocram/**
+  - tests/modules/samtools/bamtocram/**
+
 samtools/collatefastq:
   - modules/samtools/collatefastq/**
   - tests/modules/samtools/collatefastq/**
diff --git a/tests/modules/samtools/bamtocram/main.nf b/tests/modules/samtools/bamtocram/main.nf
new file mode 100644
index 00000000..b1743310
--- /dev/null
+++ b/tests/modules/samtools/bamtocram/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/bamtocram/main.nf'
+
+workflow test_samtools_bamtocram {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
+}
\ No newline at end of file
diff --git a/tests/modules/samtools/bamtocram/nextflow.config b/tests/modules/samtools/bamtocram/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/bamtocram/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/bamtocram/test.yml b/tests/modules/samtools/bamtocram/test.yml
new file mode 100644
index 00000000..3cb82902
--- /dev/null
+++ b/tests/modules/samtools/bamtocram/test.yml
@@ -0,0 +1,9 @@
+- name: samtools bamtocram test_samtools_bamtocram
+  command: nextflow run ./tests/modules/samtools/bamtocram -entry test_samtools_bamtocram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bamtocram/nextflow.config
+  tags:
+    - samtools/bamtocram
+    - samtools
+  files:
+    - path: output/samtools/test.cram
+    - path: output/samtools/test.cram.crai
+    - path: output/samtools/versions.yml

From 6a46e7cf117bbae41bca9b4c7ff7a77794df16ec Mon Sep 17 00:00:00 2001
From: Jose Espinosa-Carrasco <kadomu@gmail.com>
Date: Mon, 25 Apr 2022 19:07:43 +0200
Subject: [PATCH 28/83] Allow to pass arguments to the phantompeakqualtools
 script itself (#1562)

* Allow to pass arguments to the script itself

* Place args2 correctly

* Define args2 aaaaarrrrgggg

* Testing locally before commiting is a good practice

* Update modules/phantompeakqualtools/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 modules/phantompeakqualtools/main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf
index 0362b2e7..d8f73342 100644
--- a/modules/phantompeakqualtools/main.nf
+++ b/modules/phantompeakqualtools/main.nf
@@ -22,11 +22,12 @@ process PHANTOMPEAKQUALTOOLS {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args ?: ''
+    def args2  = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     RUN_SPP=`which run_spp.R`
-    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out"
+    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 1f77bc130b26309573670c58053a928a4602a925 Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Tue, 26 Apr 2022 16:32:20 +0200
Subject: [PATCH 29/83] Update minimap2/align module (#1537)

---
 modules/minimap2/align/main.nf        | 22 ++++++++++++++++------
 modules/minimap2/align/meta.yml       | 18 ++++++++++++++++++
 tests/modules/minimap2/align/main.nf  | 10 ++++++++--
 tests/modules/minimap2/align/test.yml | 16 ++++++++--------
 4 files changed, 50 insertions(+), 16 deletions(-)

diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf
index fe06f14d..7ba05ee9 100644
--- a/modules/minimap2/align/main.nf
+++ b/modules/minimap2/align/main.nf
@@ -2,18 +2,22 @@ process MINIMAP2_ALIGN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
-        'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
+        'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
 
     input:
     tuple val(meta), path(reads)
     path reference
+    val bam_format
+    val cigar_paf_format
+    val cigar_bam
 
     output:
-    tuple val(meta), path("*.paf"), emit: paf
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("*.paf"), optional: true, emit: paf
+    tuple val(meta), path("*.bam"), optional: true, emit: bam
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,13 +26,19 @@ process MINIMAP2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
+    def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
+    def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
+    def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
     """
     minimap2 \\
         $args \\
         -t $task.cpus \\
         $reference \\
         $input_reads \\
-        > ${prefix}.paf
+        $cigar_paf \\
+        $set_cigar_bam \\
+        $bam_output
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/minimap2/align/meta.yml b/modules/minimap2/align/meta.yml
index 89e24283..991b39a0 100644
--- a/modules/minimap2/align/meta.yml
+++ b/modules/minimap2/align/meta.yml
@@ -29,6 +29,17 @@ input:
       type: file
       description: |
         Reference database in FASTA format.
+  - bam_format:
+      type: boolean
+      description: Specify that output should be in BAM format
+  - cigar_paf_format:
+      type: boolean
+      description: Specify that output CIGAR should be in PAF format
+  - cigar_bam:
+      type: boolean
+      description: |
+        Write CIGAR with >65535 ops at the CG tag. This is recommended when
+        doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
 output:
   - meta:
       type: map
@@ -39,9 +50,16 @@ output:
       type: file
       description: Alignment in PAF format
       pattern: "*.paf"
+  - bam:
+      type: file
+      description: Alignment in BAM format
+      pattern: "*.bam"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@heuermh"
+  - "@sofstam"
+  - "@sateeshperi"
+  - "@jfy133"
diff --git a/tests/modules/minimap2/align/main.nf b/tests/modules/minimap2/align/main.nf
index e507d3e5..ee6c0838 100644
--- a/tests/modules/minimap2/align/main.nf
+++ b/tests/modules/minimap2/align/main.nf
@@ -9,8 +9,11 @@ workflow test_minimap2_align_single_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
 }
 
 workflow test_minimap2_align_paired_end {
@@ -19,6 +22,9 @@ workflow test_minimap2_align_paired_end {
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format  = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
 }
diff --git a/tests/modules/minimap2/align/test.yml b/tests/modules/minimap2/align/test.yml
index 73dd73e2..c392e313 100644
--- a/tests/modules/minimap2/align/test.yml
+++ b/tests/modules/minimap2/align/test.yml
@@ -1,17 +1,17 @@
-- name: minimap2 align single-end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+- name: minimap2 align test_minimap2_align_single_end
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
-      md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml
 
-- name: minimap2 align paired-end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+- name: minimap2 align test_minimap2_align_paired_end
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
-      md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml

From 85ec13ff1fc2196c5a507ea497de468101baabed Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Tue, 26 Apr 2022 19:15:24 +0100
Subject: [PATCH 30/83] Add Trimgalore output for unpaired reads (#1568)

* Add Trimgalore output for unpaired reads

* Use glob instead of outprefix
---
 modules/trimgalore/main.nf  | 13 ++++++++-----
 modules/trimgalore/meta.yml |  5 +++++
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf
index 9487c799..3a3fca90 100644
--- a/modules/trimgalore/main.nf
+++ b/modules/trimgalore/main.nf
@@ -11,12 +11,13 @@ process TRIMGALORE {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fq.gz")    , emit: reads
-    tuple val(meta), path("*report.txt"), emit: log
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
+    tuple val(meta), path("*report.txt")          , emit: log
+    path "versions.yml"                           , emit: versions
 
-    tuple val(meta), path("*.html"), emit: html optional true
-    tuple val(meta), path("*.zip") , emit: zip optional true
+    tuple val(meta), path("*unpaired*.fq.gz")     , emit: unpaired, optional: true
+    tuple val(meta), path("*.html")               , emit: html    , optional: true
+    tuple val(meta), path("*.zip")                , emit: zip     , optional: true
 
     when:
     task.ext.when == null || task.ext.when
@@ -52,6 +53,7 @@ process TRIMGALORE {
             $c_r1 \\
             $tpc_r1 \\
             ${prefix}.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
@@ -73,6 +75,7 @@ process TRIMGALORE {
             $tpc_r2 \\
             ${prefix}_1.fastq.gz \\
             ${prefix}_2.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
diff --git a/modules/trimgalore/meta.yml b/modules/trimgalore/meta.yml
index e99a8833..439f566d 100644
--- a/modules/trimgalore/meta.yml
+++ b/modules/trimgalore/meta.yml
@@ -37,6 +37,11 @@ output:
         List of input adapter trimmed FastQ files of size 1 and 2 for
         single-end and paired-end data, respectively.
       pattern: "*.{fq.gz}"
+  - unpaired:
+      type: file
+      description: |
+        FastQ files containing unpaired reads from read 1 or read 2
+      pattern: "*unpaired*.fq.gz"
   - html:
       type: file
       description: FastQC report (optional)

From 61e740f79cbb4538483e751ad82ca71c592f3079 Mon Sep 17 00:00:00 2001
From: Jasmin F <73216762+jasmezz@users.noreply.github.com>
Date: Wed, 27 Apr 2022 12:40:04 +0200
Subject: [PATCH 31/83] Add antismash download DB: missing container folders as
 output channels (#1567)

* Add missing container folders as output channels

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tool name

* Update test output checksum

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 .../antismashlitedownloaddatabases/main.nf    |  8 +++++--
 .../antismashlitedownloaddatabases/meta.yml   | 21 ++++++++++++++++---
 .../antismashlitedownloaddatabases/test.yml   |  7 +++++--
 3 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf
index 1853d80a..72314eee 100644
--- a/modules/antismash/antismashlitedownloaddatabases/main.nf
+++ b/modules/antismash/antismashlitedownloaddatabases/main.nf
@@ -7,8 +7,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
         'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
 
     /*
-    These files are normally downloaded by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
+    These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
     Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them.
+    These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers.
     */
 
     containerOptions {
@@ -26,6 +27,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     output:
     path("antismash_db") , emit: database
+    path("css"), emit: css_dir
+    path("detection"), emit: detection_dir
+    path("modules"), emit: modules_dir
     path "versions.yml", emit: versions
 
     when:
@@ -40,7 +44,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        antismash: \$(antismash --version | sed 's/antiSMASH //')
+        antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
     END_VERSIONS
     """
 }
diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml
index ad393bae..619dc8c2 100644
--- a/modules/antismash/antismashlitedownloaddatabases/meta.yml
+++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml
@@ -27,17 +27,17 @@ input:
   - database_css:
       type: directory
       description: |
-        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
       pattern: "css"
   - database_detection:
       type: directory
       description: |
-        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
       pattern: "detection"
   - database_modules:
       type: directory
       description: |
-        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
       pattern: "modules"
 
 output:
@@ -50,6 +50,21 @@ output:
       type: directory
       description: Download directory for antiSMASH databases
       pattern: "antismash_db"
+  - css_dir:
+      type: directory
+      description: |
+        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+      pattern: "css"
+  - detection_dir:
+      type: directory
+      description: |
+        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+      pattern: "detection"
+  - modules_dir:
+      type: directory
+      description: |
+        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+      pattern: "modules"
 
 authors:
   - "@jasmezz"
diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
index 3493bb4b..1079363c 100644
--- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
+++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
@@ -1,14 +1,17 @@
 - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
   command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
   tags:
-    - antismash/antismashlitedownloaddatabases
     - antismash
+    - antismash/antismashlitedownloaddatabases
   files:
     - path: output/antismash/versions.yml
-      md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3
+      md5sum: 24859c67023abab99de295d3675a24b6
     - path: output/antismash/antismash_db
     - path: output/antismash/antismash_db/clusterblast
     - path: output/antismash/antismash_db/clustercompare
     - path: output/antismash/antismash_db/pfam
     - path: output/antismash/antismash_db/resfam
     - path: output/antismash/antismash_db/tigrfam
+    - path: output/antismash/css
+    - path: output/antismash/detection
+    - path: output/antismash/modules

From 10ca39a86f1b227a5535238d02398fec686eba72 Mon Sep 17 00:00:00 2001
From: "Maxime U. Garcia" <max.u.garcia@gmail.com>
Date: Wed, 27 Apr 2022 16:03:44 +0200
Subject: [PATCH 32/83] add intervals possibilities to splitncigarreads (#1571)

---
 modules/gatk4/splitncigarreads/main.nf        |  4 +++-
 modules/gatk4/splitncigarreads/meta.yml       |  7 +++++++
 tests/modules/gatk4/splitncigarreads/main.nf  | 18 +++++++++++++++++-
 tests/modules/gatk4/splitncigarreads/test.yml | 11 ++++++++++-
 4 files changed, 37 insertions(+), 3 deletions(-)

diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf
index f7c559d9..85e5daa8 100644
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/modules/gatk4/splitncigarreads/main.nf
@@ -8,7 +8,7 @@ process GATK4_SPLITNCIGARREADS {
         'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai), path(intervals)
     path  fasta
     path  fai
     path  dict
@@ -23,6 +23,7 @@ process GATK4_SPLITNCIGARREADS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def interval_command = intervals ? "--intervals $intervals" : ""
 
     def avail_mem = 3
     if (!task.memory) {
@@ -35,6 +36,7 @@ process GATK4_SPLITNCIGARREADS {
         --input $bam \\
         --output ${prefix}.bam \\
         --reference $fasta \\
+        $interval_command \\
         --tmp-dir . \\
         $args
 
diff --git a/modules/gatk4/splitncigarreads/meta.yml b/modules/gatk4/splitncigarreads/meta.yml
index 407e80bd..76bfdcd3 100644
--- a/modules/gatk4/splitncigarreads/meta.yml
+++ b/modules/gatk4/splitncigarreads/meta.yml
@@ -23,6 +23,13 @@ input:
       type: list
       description: BAM/SAM/CRAM file containing reads
       pattern: "*.{bam,sam,cram}"
+  - bai:
+      type: list
+      description: BAI/SAI/CRAI index file (optional)
+      pattern: "*.{bai,sai,crai}"
+  - intervals:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
   - fasta:
       type: file
       description: The reference fasta file
diff --git a/tests/modules/gatk4/splitncigarreads/main.nf b/tests/modules/gatk4/splitncigarreads/main.nf
index 7e5b7c9a..31e45cec 100644
--- a/tests/modules/gatk4/splitncigarreads/main.nf
+++ b/tests/modules/gatk4/splitncigarreads/main.nf
@@ -6,7 +6,23 @@ include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarre
 
 workflow test_gatk4_splitncigarreads {
     input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                [],
+                []
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_splitncigarreads_intervals {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml
index c38064e2..d9a58901 100644
--- a/tests/modules/gatk4/splitncigarreads/test.yml
+++ b/tests/modules/gatk4/splitncigarreads/test.yml
@@ -5,5 +5,14 @@
     - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.bam
-      md5sum: ceed15c0bd64ff5c38d3816905933b0b
+      md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2
+    - path: output/gatk4/versions.yml
+- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
+  command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/splitncigarreads
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: cd56e3225950f519fd47164cca60a0bb
     - path: output/gatk4/versions.yml

From 213403187932dbbdd936a04474cc8cd8abae7a08 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 27 Apr 2022 18:15:11 +0100
Subject: [PATCH 33/83] Bump SAMtools version for custom/getchromsizes (#1572)

---
 modules/custom/getchromsizes/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/custom/getchromsizes/main.nf b/modules/custom/getchromsizes/main.nf
index bbcfa9be..0eabf3a4 100644
--- a/modules/custom/getchromsizes/main.nf
+++ b/modules/custom/getchromsizes/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
     tag "$fasta"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     path fasta

From 1b5d3f5ac2ae61ee35dece20a2aeb8018b6438ce Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelh@users.noreply.github.com>
Date: Wed, 27 Apr 2022 19:21:26 +0100
Subject: [PATCH 34/83] Bump STAR version to 2.7.10a for RSEM modules (#1573)

* Bump STAR version to 2.7.10a for RSEM modules

* Fix tests
---
 modules/rsem/calculateexpression/main.nf        | 6 +++---
 modules/rsem/preparereference/main.nf           | 6 +++---
 tests/config/test_data.config                   | 4 ++--
 tests/modules/rsem/calculateexpression/test.yml | 4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf
index cf147a63..1ab3a635 100644
--- a/modules/rsem/calculateexpression/main.nf
+++ b/modules/rsem/calculateexpression/main.nf
@@ -2,10 +2,10 @@ process RSEM_CALCULATEEXPRESSION {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf
index 2d2ca205..da11be45 100644
--- a/modules/rsem/preparereference/main.nf
+++ b/modules/rsem/preparereference/main.nf
@@ -2,10 +2,10 @@ process RSEM_PREPAREREFERENCE {
     tag "$fasta"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
 
     input:
     path fasta, stageAs: "rsem/*"
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index f6ea242d..b3171a51 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -245,8 +245,8 @@ params {
                 test2_2_fastq_gz                               = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
                 test2_umi_1_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
                 test2_umi_2_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
-                test_rnaseq_1_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz"
-                test_rnaseq_2_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz"
+                test_rnaseq_1_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
+                test_rnaseq_2_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
 
                 test_baserecalibrator_table                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
                 test2_baserecalibrator_table                   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
diff --git a/tests/modules/rsem/calculateexpression/test.yml b/tests/modules/rsem/calculateexpression/test.yml
index f19c3398..b0251de9 100644
--- a/tests/modules/rsem/calculateexpression/test.yml
+++ b/tests/modules/rsem/calculateexpression/test.yml
@@ -42,7 +42,7 @@
     - path: output/rsem/rsem/genome.transcripts.fa
       md5sum: 050c521a2719c2ae48267c1e65218f29
     - path: output/rsem/rsem/genomeParameters.txt
-      md5sum: 2fe3a030e1706c3e8cd4df3818e6dd2f
+      md5sum: df5a456e3242520cc36e0083a6a7d9dd
     - path: output/rsem/rsem/sjdbInfo.txt
       md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
     - path: output/rsem/rsem/sjdbList.fromGTF.out.tab
@@ -63,4 +63,4 @@
     - path: output/rsem/test.stat/test.theta
       md5sum: de2e4490c98cc5383a86ae8225fd0a28
     - path: output/rsem/test.transcript.bam
-      md5sum: 7846491086c478858419667d60f18edd
+      md5sum: ed681d39f5700ffc74d6321525330d93

From 2b29ff5883278856200f003328ece8d4897548bc Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 10:03:02 +0200
Subject: [PATCH 35/83] drop params.options

---
 subworkflows/nf-core/bam_qc_picard/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 31edb2c3..b8a92a21 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -4,9 +4,9 @@
 
 params.options = [:]
 
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picardcollectmultiplemetrics/main' addParams( options: params.options )
-include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picardcollectwgsmetrics/main'      addParams( options: params.options )
-include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picardcollecthsmetrics/main'       addParams( options: params.options )
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picardcollectmultiplemetrics/main'
+include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picardcollectwgsmetrics/main'
+include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picardcollecthsmetrics/main'
 
 workflow BAM_QC_PICARD {
     take:

From 8fb8199f3115c1a7f136202882b39be403ac5cd5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 10:05:07 +0200
Subject: [PATCH 36/83] fix copilot suggestion

---
 subworkflows/nf-core/bam_qc_picard/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index b8a92a21..e4a7e5f0 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -22,10 +22,10 @@ workflow BAM_QC_PICARD {
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     if (!ch_bait_interval.isEmpty() || !ch_target_interval.isEmpty()) {
         if (ch_bait_interval.isEmpty()) {
-            throw new Error("Bait interval channel is empty")
+            log.error("Bait interval channel is empty")
         }
         if (ch_target_interval.isEmpty()) {
-            throw new Error("Target interval channel is empty")
+            log.error("Target interval channel is empty")
         }
         PICARD_COLLECTHSMETRICS( ch_bam_bai, ch_fasta, ch_bait_interval, ch_target_interval )
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())

From 433aaece46967b56ba6a4c937ce1c8b0706b260e Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 10:05:31 +0200
Subject: [PATCH 37/83] Update tests/subworkflows/nf-core/bam_qc_picard/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 tests/subworkflows/nf-core/bam_qc_picard/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/subworkflows/nf-core/bam_qc_picard/main.nf b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
index d88f2bf9..9112416b 100644
--- a/tests/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -16,6 +16,8 @@ workflow test_bam_qc_picard_targetted {
     input = [ [ id:'test', single_end:false ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
             ]
+    bait    = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
 
-    BAM_QC_PICARD ( input, [], file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true) )
+    BAM_QC_PICARD ( input, [], bait, target )
 }

From 3cbf5c63e5677491377f23e6dda20443804a8158 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 10:09:25 +0200
Subject: [PATCH 38/83] Update subworkflows/nf-core/bam_qc_picard/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 subworkflows/nf-core/bam_qc_picard/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index e4a7e5f0..851268c6 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -20,7 +20,7 @@ workflow BAM_QC_PICARD {
 
     PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta] )
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
-    if (!ch_bait_interval.isEmpty() || !ch_target_interval.isEmpty()) {
+    if (ch_bait_interval || ch_target_interval) {
         if (ch_bait_interval.isEmpty()) {
             log.error("Bait interval channel is empty")
         }

From 881e9db4bfde569c8e9c0d51a1b3916817610fc0 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 10:19:30 +0200
Subject: [PATCH 39/83] update tests

---
 subworkflows/nf-core/bam_qc_picard/meta.yml       |  2 +-
 tests/subworkflows/nf-core/bam_qc_picard/main.nf  | 12 +++++++-----
 tests/subworkflows/nf-core/bam_qc_picard/test.yml |  2 +-
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
index 77104e82..c4422150 100644
--- a/subworkflows/nf-core/bam_qc_picard/meta.yml
+++ b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -47,7 +47,7 @@ output:
   - hs_metrics:
       type: file
       description: Alignment metrics files generated by picard CollectHsMetrics
-      pattern: "*_collecthsmetrics.txt"
+      pattern: "*_metrics.txt"
   - wgs_metrics:
       type: file
       description: Alignment metrics files generated by picard CollectWgsMetrics
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/main.nf b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
index 9112416b..03696b44 100644
--- a/tests/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -6,18 +6,20 @@ include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/m
 
 workflow test_bam_qc_picard_wgs {
     input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
+    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BAM_QC_PICARD ( input, [], [], [] )
+    BAM_QC_PICARD ( input, fasta, [], [] )
 }
 
 workflow test_bam_qc_picard_targetted {
     input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
+    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     bait    = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
-    target = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+    target  = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
 
-    BAM_QC_PICARD ( input, [], bait, target )
+    BAM_QC_PICARD ( input, fasta, bait, target )
 }
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/test.yml b/tests/subworkflows/nf-core/bam_qc_picard/test.yml
index af98230d..7b0a6c2b 100644
--- a/tests/subworkflows/nf-core/bam_qc_picard/test.yml
+++ b/tests/subworkflows/nf-core/bam_qc_picard/test.yml
@@ -30,4 +30,4 @@
     - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
     - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
     - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-    - path: ./output/picard/test_collecthsmetrics.txt
+    - path: ./output/picard/test.CollectHsMetrics.coverage_metrics

From b92efb7abfc77cb8d9b4149c5fb866409122ce05 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 10:21:47 +0200
Subject: [PATCH 40/83] add nextflow.config

---
 tests/subworkflows/nf-core/bam_qc_picard/nextflow.config | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 tests/subworkflows/nf-core/bam_qc_picard/nextflow.config

diff --git a/tests/subworkflows/nf-core/bam_qc_picard/nextflow.config b/tests/subworkflows/nf-core/bam_qc_picard/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/subworkflows/nf-core/bam_qc_picard/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

From dee8ec9e911ec848e93c8ed0b9667e7c674e9132 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 12:53:17 +0200
Subject: [PATCH 41/83] fix typos

---
 subworkflows/nf-core/bam_qc_picard/main.nf | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 851268c6..747d5995 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -2,11 +2,9 @@
 // Run QC steps on BAM/CRAM files using Picard
 //
 
-params.options = [:]
-
-include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picardcollectmultiplemetrics/main'
-include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picardcollectwgsmetrics/main'
-include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picardcollecthsmetrics/main'
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picard/collectmultiplemetrics/main'
+include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picard/collectwgsmetrics/main'
+include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picard/collecthsmetrics/main'
 
 workflow BAM_QC_PICARD {
     take:
@@ -18,7 +16,7 @@ workflow BAM_QC_PICARD {
     main:
     ch_versions = Channel.empty()
 
-    PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta] )
+    PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta )
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     if (ch_bait_interval || ch_target_interval) {
         if (ch_bait_interval.isEmpty()) {

From 68f1c27169946f931ea4318911de5681f88b2961 Mon Sep 17 00:00:00 2001
From: Praveen Raj S <43108054+praveenraj2018@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:41:20 +0200
Subject: [PATCH 42/83] Changed tbi as optional output in GATK4 HaplotypeCaller
 (#1576)

* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.

* Apply suggestions from code review

* Update modules/gatk4/haplotypecaller/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 modules/gatk4/haplotypecaller/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf
index 57f69ecd..2cd9e7d4 100644
--- a/modules/gatk4/haplotypecaller/main.nf
+++ b/modules/gatk4/haplotypecaller/main.nf
@@ -17,7 +17,7 @@ process GATK4_HAPLOTYPECALLER {
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
-    tuple val(meta), path("*.tbi")   , emit: tbi
+    tuple val(meta), path("*.tbi")   , optional:true, emit: tbi
     path "versions.yml"              , emit: versions
 
     when:

From e0a8af869324765ec0c6a375703bfa68f5ba4e77 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:42:14 +0200
Subject: [PATCH 43/83] fix outputs

---
 subworkflows/nf-core/bam_qc_picard/main.nf  | 14 ++++++++------
 subworkflows/nf-core/bam_qc_picard/meta.yml |  8 ++------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 747d5995..13f4a845 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -8,7 +8,7 @@ include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picard/collecth
 
 workflow BAM_QC_PICARD {
     take:
-    ch_bam_bai          // channel: [ val(meta), [ bam ], [bai/csi] ]
+    ch_bam              // channel: [ val(meta), [ bam ]]
     ch_fasta            // channel: [ fasta ]
     ch_bait_interval    // channel: [ bait_interval ]
     ch_target_interval  // channel: [ target_interval ]
@@ -16,7 +16,7 @@ workflow BAM_QC_PICARD {
     main:
     ch_versions = Channel.empty()
 
-    PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta )
+    PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     if (ch_bait_interval || ch_target_interval) {
         if (ch_bait_interval.isEmpty()) {
@@ -25,16 +25,18 @@ workflow BAM_QC_PICARD {
         if (ch_target_interval.isEmpty()) {
             log.error("Target interval channel is empty")
         }
-        PICARD_COLLECTHSMETRICS( ch_bam_bai, ch_fasta, ch_bait_interval, ch_target_interval )
+        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_bait_interval, ch_target_interval )
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
-        PICARD_COLLECTWGSMETRICS( ch_bam_bai, ch_fasta )
+        PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
     }
 
+    ch_coverage_metrics = Channel.empty()
+    ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first(), PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
+
     emit:
-    hs_metrics          = PICARD_COLLECTHSMETRICS.out.hs_metrics    // channel: [ val(meta), [ hs_metrics ] ]
-    wgs_metrics         = PICARD_COLLECTWGSMETRICS.out.metrics      // channel: [ val(meta), [ wgs_metrics ] ]
+    coverage_metrics    = PICARD_COLLECTWGSMETRICS.out.metrics      // channel: [ val(meta), [ coverage_metrics ] ]
     multiple_metrics    = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
 
     versions = ch_versions                                          // channel: [ versions.yml ]
diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
index c4422150..67d3496e 100644
--- a/subworkflows/nf-core/bam_qc_picard/meta.yml
+++ b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -44,14 +44,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - hs_metrics:
+  - coverage_metrics:
       type: file
-      description: Alignment metrics files generated by picard CollectHsMetrics
+      description: Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics
       pattern: "*_metrics.txt"
-  - wgs_metrics:
-      type: file
-      description: Alignment metrics files generated by picard CollectWgsMetrics
-      pattern: "*_{metrics}"
   - multiple_metrics:
       type: file
       description: Alignment metrics files generated by picard CollectMultipleMetrics

From 55dfe1d8ab35873790c13ee4eb75af818fef80b2 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:43:59 +0200
Subject: [PATCH 44/83] fix hsmetrics input

---
 subworkflows/nf-core/bam_qc_picard/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 13f4a845..9e429448 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -25,7 +25,7 @@ workflow BAM_QC_PICARD {
         if (ch_target_interval.isEmpty()) {
             log.error("Target interval channel is empty")
         }
-        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_bait_interval, ch_target_interval )
+        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, [], ch_bait_interval, ch_target_interval )
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )

From 8ad861a645e86c411b47472616a924063afba106 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:52:03 +0200
Subject: [PATCH 45/83] add fasta index

---
 subworkflows/nf-core/bam_qc_picard/main.nf       | 12 +++++++-----
 subworkflows/nf-core/bam_qc_picard/meta.yml      | 10 +++++-----
 tests/subworkflows/nf-core/bam_qc_picard/main.nf | 12 +++++++-----
 3 files changed, 19 insertions(+), 15 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 9e429448..e6f82feb 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -10,14 +10,17 @@ workflow BAM_QC_PICARD {
     take:
     ch_bam              // channel: [ val(meta), [ bam ]]
     ch_fasta            // channel: [ fasta ]
+    ch_fasta_faix       // channel: [ fasta_fai ]
     ch_bait_interval    // channel: [ bait_interval ]
     ch_target_interval  // channel: [ target_interval ]
 
     main:
     ch_versions = Channel.empty()
+    ch_coverage_metrics = Channel.empty()
 
     PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+
     if (ch_bait_interval || ch_target_interval) {
         if (ch_bait_interval.isEmpty()) {
             log.error("Bait interval channel is empty")
@@ -26,18 +29,17 @@ workflow BAM_QC_PICARD {
             log.error("Target interval channel is empty")
         }
         PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, [], ch_bait_interval, ch_target_interval )
+        ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
+        ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
     }
 
-    ch_coverage_metrics = Channel.empty()
-    ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first(), PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
-
     emit:
-    coverage_metrics    = PICARD_COLLECTWGSMETRICS.out.metrics      // channel: [ val(meta), [ coverage_metrics ] ]
+    coverage_metrics    = ch_coverage_metrics                       // channel: [ val(meta), [ coverage_metrics ] ]
     multiple_metrics    = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
 
-    versions = ch_versions                                          // channel: [ versions.yml ]
+    versions            = ch_versions                               // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
index 67d3496e..c45215d1 100644
--- a/subworkflows/nf-core/bam_qc_picard/meta.yml
+++ b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -22,14 +22,14 @@ input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
-  - bai:
-      type: file
-      description: Index for BAM/CRAM/SAM file
-      pattern: "*.{bai,crai,sai}"
   - fasta:
       type: optional file
-      description: Reference file the CRAM was created with
+      description: Reference fasta file
       pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: optional file
+      description: Reference fasta file index
+      pattern: "*.{fasta,fa}.fai"
   - bait_intervals:
       type: optional file
       description: An interval list file that contains the locations of the baits used.
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/main.nf b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
index 03696b44..a3e2ed62 100644
--- a/tests/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -9,17 +9,19 @@ workflow test_bam_qc_picard_wgs {
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
     fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    BAM_QC_PICARD ( input, fasta, [], [] )
+    BAM_QC_PICARD ( input, fasta, fasta_fai, [], [] )
 }
 
 workflow test_bam_qc_picard_targetted {
     input = [ [ id:'test', single_end:false ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
-    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    bait    = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
-    target  = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bait        = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target      = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
 
-    BAM_QC_PICARD ( input, fasta, bait, target )
+    BAM_QC_PICARD ( input, fasta, fasta_fai, bait, target )
 }

From 2fc857955f42c3aed840f9a61062b481a159ff4a Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:53:48 +0200
Subject: [PATCH 46/83] fix index omission

---
 subworkflows/nf-core/bam_qc_picard/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index e6f82feb..341a4310 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -10,7 +10,7 @@ workflow BAM_QC_PICARD {
     take:
     ch_bam              // channel: [ val(meta), [ bam ]]
     ch_fasta            // channel: [ fasta ]
-    ch_fasta_faix       // channel: [ fasta_fai ]
+    ch_fasta_fai        // channel: [ fasta_fai ]
     ch_bait_interval    // channel: [ bait_interval ]
     ch_target_interval  // channel: [ target_interval ]
 
@@ -28,7 +28,7 @@ workflow BAM_QC_PICARD {
         if (ch_target_interval.isEmpty()) {
             log.error("Target interval channel is empty")
         }
-        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, [], ch_bait_interval, ch_target_interval )
+        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
         ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {

From 4618c542e9d64cd71176cfd24fe0edc908eb3d10 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:59:46 +0200
Subject: [PATCH 47/83] fix metrics output

---
 subworkflows/nf-core/bam_qc_picard/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 341a4310..b8be04b2 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -29,12 +29,12 @@ workflow BAM_QC_PICARD {
             log.error("Target interval channel is empty")
         }
         PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
-        ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first())
+        ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
-        ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
+        ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics.first())
     }
 
     emit:

From 57cb730e78634673fb254a77606e014ce942734c Mon Sep 17 00:00:00 2001
From: Daniel Cooke <daniel.cooke@invitae.com>
Date: Thu, 28 Apr 2022 13:06:38 +0100
Subject: [PATCH 48/83] Fix tiddit/sv (#1580)

* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
---
 modules/tiddit/sv/main.nf        | 2 +-
 tests/modules/tiddit/sv/test.yml | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/tiddit/sv/main.nf b/modules/tiddit/sv/main.nf
index 1bf7146a..b3e3813c 100644
--- a/modules/tiddit/sv/main.nf
+++ b/modules/tiddit/sv/main.nf
@@ -24,7 +24,7 @@ process TIDDIT_SV {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
+    def reference = fasta ? "--ref $fasta" : ""
     """
     tiddit \\
         --sv \\
diff --git a/tests/modules/tiddit/sv/test.yml b/tests/modules/tiddit/sv/test.yml
index 168d21c5..40ea5b4d 100644
--- a/tests/modules/tiddit/sv/test.yml
+++ b/tests/modules/tiddit/sv/test.yml
@@ -9,6 +9,7 @@
     - path: output/tiddit/test.signals.tab
       md5sum: dab4b2fec4ddf8eb1c23005b0770150e
     - path: output/tiddit/test.vcf
+      md5sum: bdce14ae8292bf3deb81f6f255baf859
 
 - name: tiddit sv no ref
   command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
@@ -21,3 +22,4 @@
     - path: output/tiddit/test.signals.tab
       md5sum: dab4b2fec4ddf8eb1c23005b0770150e
     - path: output/tiddit/test.vcf
+      md5sum: 3d0e83a8199b2bdb81cfe3e6b12bf64b

From cdefbec66999c0b49d8bfeea9d6f9d19056635a2 Mon Sep 17 00:00:00 2001
From: JIANHONG OU <jianhong@users.noreply.github.com>
Date: Thu, 28 Apr 2022 08:16:26 -0400
Subject: [PATCH 49/83] add kimporttext module (#1560)

* add kimporttext module

* fix the Prettier error.

* fix the Prettier error.

* fix the test.yml

* fix the test.yml

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* update the test files;
simplify the main script of krona/ktimporttext.

* update the test file url for krona ktimporttext

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/krona/ktimporttext/main.nf            | 34 ++++++++++++++
 modules/krona/ktimporttext/meta.yml           | 47 +++++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/config/test_data.config                 |  3 ++
 tests/modules/krona/ktimporttext/main.nf      | 31 ++++++++++++
 .../krona/ktimporttext/nextflow.config        |  5 ++
 tests/modules/krona/ktimporttext/test.yml     | 19 ++++++++
 7 files changed, 143 insertions(+)
 create mode 100644 modules/krona/ktimporttext/main.nf
 create mode 100644 modules/krona/ktimporttext/meta.yml
 create mode 100644 tests/modules/krona/ktimporttext/main.nf
 create mode 100644 tests/modules/krona/ktimporttext/nextflow.config
 create mode 100644 tests/modules/krona/ktimporttext/test.yml

diff --git a/modules/krona/ktimporttext/main.nf b/modules/krona/ktimporttext/main.nf
new file mode 100644
index 00000000..de0cfc22
--- /dev/null
+++ b/modules/krona/ktimporttext/main.nf
@@ -0,0 +1,34 @@
+process KRONA_KTIMPORTTEXT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
+        'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(report)
+
+    output:
+    tuple val(meta), path ('*.html'), emit: html
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    ktImportText  \\
+        $args \\
+        -o ${prefix}.html \\
+        $report
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/krona/ktimporttext/meta.yml b/modules/krona/ktimporttext/meta.yml
new file mode 100644
index 00000000..a7108e0d
--- /dev/null
+++ b/modules/krona/ktimporttext/meta.yml
@@ -0,0 +1,47 @@
+name: "krona_ktimporttext"
+description: Creates a Krona chart from text files listing quantities and lineages.
+keywords:
+  - plot
+  - taxonomy
+  - interactive
+  - html
+  - visualisation
+  - krona chart
+  - metagenomics
+tools:
+  - krona:
+      description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
+      homepage: https://github.com/marbl/Krona/wiki/KronaTools
+      documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
+      tool_dev_url: https://github.com/marbl/Krona
+      doi: 10.1186/1471-2105-12-385
+      licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - report:
+      type: file
+      description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored."
+      pattern: "*.{txt}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - html:
+      type: file
+      description: A html file containing an interactive krona plot.
+      pattern: "*.{html}"
+
+authors:
+  - "@jianhong"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4d8ce0b5..dfcbfa8c 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1050,6 +1050,10 @@ krona/ktimporttaxonomy:
   - modules/krona/ktimporttaxonomy/**
   - tests/modules/krona/ktimporttaxonomy/**
 
+krona/ktimporttext:
+  - modules/krona/ktimporttext/**
+  - tests/modules/krona/ktimporttext/**
+
 last/dotplot:
   - modules/last/dotplot/**
   - tests/modules/last/dotplot/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index b3171a51..5d5535c4 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -109,6 +109,9 @@ params {
 
                 test_sequencing_summary                        = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
             }
+            'metagenome' {
+                kraken_report                                  = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
+            }
         }
         'homo_sapiens' {
             'genome' {
diff --git a/tests/modules/krona/ktimporttext/main.nf b/tests/modules/krona/ktimporttext/main.nf
new file mode 100644
index 00000000..3d288b7b
--- /dev/null
+++ b/tests/modules/krona/ktimporttext/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTIMPORTTEXT } from '../../../../modules/krona/ktimporttext/main.nf'
+
+workflow test_krona_ktimporttext_multi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/ktimporttext.txt', checkIfExists: true), // krona default test file
+            file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true), //Kraken2 report file
+            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/kaiju_out4krona.txt', checkIfExists: true) // Kaiju output 4 krona
+        ]
+    ]
+
+    KRONA_KTIMPORTTEXT ( input )
+}
+
+workflow test_krona_ktimporttext_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file('http://krona.sourceforge.net/examples/text.txt', checkIfExists: true) // krona default test file
+        ]
+    ]
+
+    KRONA_KTIMPORTTEXT ( input )
+}
diff --git a/tests/modules/krona/ktimporttext/nextflow.config b/tests/modules/krona/ktimporttext/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/krona/ktimporttext/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/krona/ktimporttext/test.yml b/tests/modules/krona/ktimporttext/test.yml
new file mode 100644
index 00000000..93ae12da
--- /dev/null
+++ b/tests/modules/krona/ktimporttext/test.yml
@@ -0,0 +1,19 @@
+- name: krona ktimporttext test_krona_ktimporttext_multi
+  command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_multi -c tests/config/nextflow.config
+  tags:
+    - krona
+    - krona/ktimporttext
+  files:
+    - path: output/krona/test.html
+      contains:
+        - "DOCTYPE html PUBLIC"
+
+- name: krona ktimporttext test_krona_ktimporttext_single
+  command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_single -c tests/config/nextflow.config
+  tags:
+    - krona
+    - krona/ktimporttext
+  files:
+    - path: output/krona/test.html
+      contains:
+        - "DOCTYPE html PUBLIC"

From b3e9b88e80880f450ad79a95b2b7aa05e1de5484 Mon Sep 17 00:00:00 2001
From: Praveen Raj S <43108054+praveenraj2018@users.noreply.github.com>
Date: Thu, 28 Apr 2022 14:41:01 +0200
Subject: [PATCH 50/83] csi output in TABIX (#1579)

* Added: csi output to TABIX

* Added: tests for csi

* Fix tiddit/sv (#1580)

* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>

* Fix: prettier issues

Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
---
 modules/tabix/tabix/main.nf               |  3 ++-
 modules/tabix/tabix/meta.yml              |  4 ++++
 tests/modules/tabix/tabix/main.nf         | 19 ++++++++++++++-----
 tests/modules/tabix/tabix/nextflow.config |  6 +++++-
 tests/modules/tabix/tabix/test.yml        | 10 +++++++++-
 5 files changed, 34 insertions(+), 8 deletions(-)

diff --git a/modules/tabix/tabix/main.nf b/modules/tabix/tabix/main.nf
index c9dab068..e155e468 100644
--- a/modules/tabix/tabix/main.nf
+++ b/modules/tabix/tabix/main.nf
@@ -11,7 +11,8 @@ process TABIX_TABIX {
     tuple val(meta), path(tab)
 
     output:
-    tuple val(meta), path("*.tbi"), emit: tbi
+    tuple val(meta), path("*.tbi"), optional:true, emit: tbi
+    tuple val(meta), path("*.csi"), optional:true, emit: csi
     path  "versions.yml"          , emit: versions
 
     when:
diff --git a/modules/tabix/tabix/meta.yml b/modules/tabix/tabix/meta.yml
index 89478abe..fcc6e524 100644
--- a/modules/tabix/tabix/meta.yml
+++ b/modules/tabix/tabix/meta.yml
@@ -31,6 +31,10 @@ output:
       type: file
       description: tabix index file
       pattern: "*.{tbi}"
+  - csi:
+      type: file
+      description: coordinate sorted index file
+      pattern: "*.{csi}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/tabix/tabix/main.nf b/tests/modules/tabix/tabix/main.nf
index 993ee812..da26f4d7 100644
--- a/tests/modules/tabix/tabix/main.nf
+++ b/tests/modules/tabix/tabix/main.nf
@@ -2,9 +2,10 @@
 
 nextflow.enable.dsl = 2
 
-include { TABIX_TABIX as TABIX_BED } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_GFF } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_VCF } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_BED     } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_GFF     } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/tabix/tabix/main.nf'
 
 workflow test_tabix_tabix_bed {
     input = [ [ id:'B.bed' ], // meta map
@@ -22,10 +23,18 @@ workflow test_tabix_tabix_gff {
     TABIX_GFF ( input )
 }
 
-workflow test_tabix_tabix_vcf {
+workflow test_tabix_tabix_vcf_tbi {
     input = [ [ id:'test.vcf' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] 
             ]
 
-    TABIX_VCF ( input )
+    TABIX_VCF_TBI ( input )
+}
+
+workflow test_tabix_tabix_vcf_csi {
+    input = [ [ id:'test.vcf' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+            ]
+
+    TABIX_VCF_CSI ( input )
 }
diff --git a/tests/modules/tabix/tabix/nextflow.config b/tests/modules/tabix/tabix/nextflow.config
index aa97a873..139e0865 100644
--- a/tests/modules/tabix/tabix/nextflow.config
+++ b/tests/modules/tabix/tabix/nextflow.config
@@ -10,8 +10,12 @@ process {
         ext.args = '-p gff'
     }
 
-    withName: TABIX_VCF {
+    withName: TABIX_VCF_TBI {
         ext.args = '-p vcf'
     }
 
+   withName: TABIX_VCF_CSI {
+        ext.args = '-p vcf --csi'
+    }
+
 }
diff --git a/tests/modules/tabix/tabix/test.yml b/tests/modules/tabix/tabix/test.yml
index 46be28dd..6d168ef5 100644
--- a/tests/modules/tabix/tabix/test.yml
+++ b/tests/modules/tabix/tabix/test.yml
@@ -15,10 +15,18 @@
     - path: ./output/tabix/genome.gff3.gz.tbi
       md5sum: f79a67d95a98076e04fbe0455d825926
 - name: tabix tabix vcf
-  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
+  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
   tags:
     - tabix
     - tabix/tabix
   files:
     - path: output/tabix/test.vcf.gz.tbi
       md5sum: 36e11bf96ed0af4a92caa91a68612d64
+- name: tabix tabix vcf csi
+  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: output/tabix/test.vcf.gz.csi
+      md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd

From 6ca6de91f8da9b8cc9a34f7ef6469eb0f851604d Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 07:47:24 +0200
Subject: [PATCH 51/83] bump picard version across the board

---
 modules/picard/addorreplacereadgroups/main.nf   | 6 +++---
 modules/picard/cleansam/main.nf                 | 6 +++---
 modules/picard/collecthsmetrics/main.nf         | 6 +++---
 modules/picard/collectmultiplemetrics/main.nf   | 6 +++---
 modules/picard/collectwgsmetrics/main.nf        | 6 +++---
 modules/picard/createsequencedictionary/main.nf | 6 +++---
 modules/picard/crosscheckfingerprints/main.nf   | 6 +++---
 modules/picard/filtersamreads/main.nf           | 6 +++---
 modules/picard/fixmateinformation/main.nf       | 6 +++---
 modules/picard/liftovervcf/main.nf              | 6 +++---
 modules/picard/markduplicates/main.nf           | 6 +++---
 modules/picard/mergesamfiles/main.nf            | 6 +++---
 modules/picard/sortsam/main.nf                  | 6 +++---
 modules/picard/sortvcf/main.nf                  | 6 +++---
 14 files changed, 42 insertions(+), 42 deletions(-)

diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf
index 8e1d10af..e395f4d7 100644
--- a/modules/picard/addorreplacereadgroups/main.nf
+++ b/modules/picard/addorreplacereadgroups/main.nf
@@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf
index fb435911..4cd4db58 100644
--- a/modules/picard/cleansam/main.nf
+++ b/modules/picard/cleansam/main.nf
@@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index ef7a9b9f..26ba8a04 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index 340463a8..0c79b7a5 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index f4efaa4c..ef53d7bd 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf
index 96069e9f..3a8f1477 100644
--- a/modules/picard/createsequencedictionary/main.nf
+++ b/modules/picard/createsequencedictionary/main.nf
@@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/picard/crosscheckfingerprints/main.nf b/modules/picard/crosscheckfingerprints/main.nf
index b3dface5..d3b59402 100644
--- a/modules/picard/crosscheckfingerprints/main.nf
+++ b/modules/picard/crosscheckfingerprints/main.nf
@@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input1)
diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf
index ab75abfa..adedcdc2 100644
--- a/modules/picard/filtersamreads/main.nf
+++ b/modules/picard/filtersamreads/main.nf
@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)
diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf
index 763f3bb4..1993e4fd 100644
--- a/modules/picard/fixmateinformation/main.nf
+++ b/modules/picard/fixmateinformation/main.nf
@@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf
index cdbd637e..7ce694e9 100644
--- a/modules/picard/liftovervcf/main.nf
+++ b/modules/picard/liftovervcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index e754a587..b9fec576 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index ef5c3980..7b0185cd 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf
index adec17cb..cee60fd1 100644
--- a/modules/picard/sortsam/main.nf
+++ b/modules/picard/sortsam/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf
index 4047545e..5fe0ecfd 100644
--- a/modules/picard/sortvcf/main.nf
+++ b/modules/picard/sortvcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTVCF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)

From 00467ac64affbbc17b255762f10a6c8fa362aabc Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 07:57:11 +0200
Subject: [PATCH 52/83] update command line syntax for all tools

---
 modules/picard/addorreplacereadgroups/main.nf   |  2 +-
 modules/picard/collecthsmetrics/main.nf         |  8 ++++----
 modules/picard/collectmultiplemetrics/main.nf   |  6 +++---
 modules/picard/collectwgsmetrics/main.nf        |  6 +++---
 modules/picard/createsequencedictionary/main.nf |  4 ++--
 modules/picard/liftovervcf/main.nf              | 10 +++++-----
 modules/picard/markduplicates/main.nf           |  6 +++---
 7 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf
index e395f4d7..55200d2e 100644
--- a/modules/picard/addorreplacereadgroups/main.nf
+++ b/modules/picard/addorreplacereadgroups/main.nf
@@ -43,7 +43,7 @@ process PICARD_ADDORREPLACEREADGROUPS {
         -PL ${PLATFORM} \\
         -PU ${BARCODE} \\
         -SM ${SAMPLE} \\
-        -CREATE_INDEX true
+        --CREATE_INDEX true
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index 26ba8a04..317aff4b 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -38,10 +38,10 @@ process PICARD_COLLECTHSMETRICS {
         CollectHsMetrics \\
         $args \\
         $reference \\
-        -BAIT_INTERVALS $bait_intervals \\
-        -TARGET_INTERVALS $target_intervals \\
-        -INPUT $bam \\
-        -OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
+        --BAIT_INTERVALS $bait_intervals \\
+        --TARGET_INTERVALS $target_intervals \\
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
 
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index 0c79b7a5..a653b549 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -33,9 +33,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         -Xmx${avail_mem}g \\
         CollectMultipleMetrics \\
         $args \\
-        INPUT=$bam \\
-        OUTPUT=${prefix}.CollectMultipleMetrics \\
-        REFERENCE_SEQUENCE=$fasta
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectMultipleMetrics \\
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index ef53d7bd..957c8058 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -32,9 +32,9 @@ process PICARD_COLLECTWGSMETRICS {
         -Xmx${avail_mem}g \\
         CollectWgsMetrics \\
         $args \\
-        INPUT=$bam \\
-        OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
-        REFERENCE_SEQUENCE=$fasta
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf
index 3a8f1477..3a8bb62a 100644
--- a/modules/picard/createsequencedictionary/main.nf
+++ b/modules/picard/createsequencedictionary/main.nf
@@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
         -Xmx${avail_mem}g \\
         CreateSequenceDictionary  \\
         $args \\
-        R=$fasta \\
-        O=${prefix}.dict
+        -R $fasta \\
+        -O ${prefix}.dict
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf
index 7ce694e9..ea3f4cb7 100644
--- a/modules/picard/liftovervcf/main.nf
+++ b/modules/picard/liftovervcf/main.nf
@@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
         -Xmx${avail_mem}g \\
         LiftoverVcf \\
         $args \\
-        I=$input_vcf \\
-        O=${prefix}.lifted.vcf.gz \\
-        CHAIN=$chain \\
-        REJECT=${prefix}.unlifted.vcf.gz \\
-        R=$fasta
+        -I $input_vcf \\
+        -O ${prefix}.lifted.vcf.gz \\
+        --CHAIN $chain \\
+        --REJECT ${prefix}.unlifted.vcf.gz \\
+        -R $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index b9fec576..58b6b88a 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
         -Xmx${avail_mem}g \\
         MarkDuplicates \\
         $args \\
-        I=$bam \\
-        O=${prefix}.bam \\
-        M=${prefix}.MarkDuplicates.metrics.txt
+        -I $bam \\
+        -O ${prefix}.bam \\
+        -M ${prefix}.MarkDuplicates.metrics.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From b72ec05d69140c6a9c6054175d1412b2f116466f Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 08:19:42 +0200
Subject: [PATCH 53/83] drop md5sum from versions.yml

---
 tests/modules/picard/addorreplacereadgroups/test.yml   | 1 -
 tests/modules/picard/cleansam/test.yml                 | 1 -
 tests/modules/picard/createsequencedictionary/test.yml | 1 -
 3 files changed, 3 deletions(-)

diff --git a/tests/modules/picard/addorreplacereadgroups/test.yml b/tests/modules/picard/addorreplacereadgroups/test.yml
index aa1536bb..6ee81737 100644
--- a/tests/modules/picard/addorreplacereadgroups/test.yml
+++ b/tests/modules/picard/addorreplacereadgroups/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: 7b82f3461c2d80fc6a10385e78c9427f
     - path: output/picard/versions.yml
-      md5sum: 8a2d176295e1343146ea433c79bb517f
diff --git a/tests/modules/picard/cleansam/test.yml b/tests/modules/picard/cleansam/test.yml
index 3b235d07..08dcd84d 100644
--- a/tests/modules/picard/cleansam/test.yml
+++ b/tests/modules/picard/cleansam/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: a48f8e77a1480445efc57570c3a38a68
     - path: output/picard/versions.yml
-      md5sum: e6457d7c6de51bf6f4b577eda65e57ac
diff --git a/tests/modules/picard/createsequencedictionary/test.yml b/tests/modules/picard/createsequencedictionary/test.yml
index 2a43be41..59f2dd44 100644
--- a/tests/modules/picard/createsequencedictionary/test.yml
+++ b/tests/modules/picard/createsequencedictionary/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.dict
       contains: ["SN:MT192765.1"]
     - path: output/picard/versions.yml
-      md5sum: b3d8c7ea65b8a6d3237b153d13fe2014

From ec10f98d558a84da79ba7c90c2d57f6c6f0f7af5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 09:32:32 +0200
Subject: [PATCH 54/83] picard CollectWgsMetrics: update to new cli args
 (#1578)

* update to new cli args

* remove bam index from tuple, not needed by program

* bump picard version

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
---
 modules/picard/collectwgsmetrics/main.nf       | 14 +++++++-------
 tests/modules/picard/collectwgsmetrics/main.nf |  3 +--
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index f4efaa4c..d9c1ec7c 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam)
     path  fasta
 
     output:
@@ -32,9 +32,9 @@ process PICARD_COLLECTWGSMETRICS {
         -Xmx${avail_mem}g \\
         CollectWgsMetrics \\
         $args \\
-        INPUT=$bam \\
-        OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
-        REFERENCE_SEQUENCE=$fasta
+        -INPUT $bam \\
+        -OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
+        -REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/picard/collectwgsmetrics/main.nf b/tests/modules/picard/collectwgsmetrics/main.nf
index 1d75a2bd..eddf5603 100644
--- a/tests/modules/picard/collectwgsmetrics/main.nf
+++ b/tests/modules/picard/collectwgsmetrics/main.nf
@@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
 
 workflow test_picard_collectwgsmetrics {
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 

From 1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b Mon Sep 17 00:00:00 2001
From: Lauri Mesilaakso <john.mesilaakso@gmail.com>
Date: Fri, 29 Apr 2022 09:37:23 +0200
Subject: [PATCH 55/83] Fix typo (#1586)

---
 modules/minimap2/align/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf
index 7ba05ee9..08ac6eef 100644
--- a/modules/minimap2/align/main.nf
+++ b/modules/minimap2/align/main.nf
@@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
     def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
-    def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
-    def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
+    def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
+    def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
     """
     minimap2 \\
         $args \\

From 0e01d703ea55899bd048689258d22c153d39b981 Mon Sep 17 00:00:00 2001
From: CMGG ICT Team <ict@cmgg.be>
Date: Fri, 29 Apr 2022 10:12:52 +0200
Subject: [PATCH 56/83] remove version md5sum from fixmateinformation

---
 tests/modules/picard/fixmateinformation/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/picard/fixmateinformation/test.yml b/tests/modules/picard/fixmateinformation/test.yml
index f12f823b..f2f9c491 100644
--- a/tests/modules/picard/fixmateinformation/test.yml
+++ b/tests/modules/picard/fixmateinformation/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: 746102e8c242c0ef42e045c49d320030
     - path: output/picard/versions.yml
-      md5sum: 4329ba7cdca8f4f6018dfd5c019ba2eb

From bda132191db9548cd1fc1c594399cba583bcd061 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 10:13:22 +0200
Subject: [PATCH 57/83] fix args in nextflow.config

---
 tests/modules/picard/markduplicates/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/picard/markduplicates/nextflow.config b/tests/modules/picard/markduplicates/nextflow.config
index 9178c5b1..40d46110 100644
--- a/tests/modules/picard/markduplicates/nextflow.config
+++ b/tests/modules/picard/markduplicates/nextflow.config
@@ -3,7 +3,7 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: PICARD_MARKDUPLICATES_UNSORTED {
-        ext.args = 'ASSUME_SORT_ORDER=queryname'
+        ext.args = '--ASSUME_SORT_ORDER queryname'
     }
 
 }

From b2e4342105d4e6b06edd33ed2613328eb740b4b8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 10:21:22 +0200
Subject: [PATCH 58/83] fix args in nextflow.config

---
 tests/modules/picard/liftovervcf/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/picard/liftovervcf/nextflow.config b/tests/modules/picard/liftovervcf/nextflow.config
index e1581bb9..f69fc351 100644
--- a/tests/modules/picard/liftovervcf/nextflow.config
+++ b/tests/modules/picard/liftovervcf/nextflow.config
@@ -1,5 +1,5 @@
 process {
-    ext.args = "WARN_ON_MISSING_CONTIG=true"
+    ext.args = "--WARN_ON_MISSING_CONTIG true"
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
 }

From 42564565b934eeb2449e35ec97ed13ff2a67f1de Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 29 Apr 2022 10:26:17 +0200
Subject: [PATCH 59/83] Update diamond/blastx diamond/blastp to support all
 possible output formats

---
 modules/diamond/blastp/main.nf        | 17 ++++++++++++++---
 modules/diamond/blastp/meta.yml       |  9 +++++++++
 modules/diamond/blastx/main.nf        | 17 ++++++++++++++---
 modules/diamond/blastx/meta.yml       |  9 +++++++++
 tests/modules/diamond/blastp/main.nf  | 13 ++++++++++++-
 tests/modules/diamond/blastp/test.yml | 21 ++++++++++++++++++---
 tests/modules/diamond/blastx/main.nf  | 13 ++++++++++++-
 tests/modules/diamond/blastx/test.yml | 24 ++++++++++++++++++++----
 8 files changed, 108 insertions(+), 15 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index 955952dc..d7c53d6f 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -11,10 +11,11 @@ process DIAMOND_BLASTP {
 
     input:
     tuple val(meta), path(fasta)
-    path  db
+    path db
+    val outext
 
     output:
-    tuple val(meta), path('*.txt'), emit: txt
+    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
     path "versions.yml"           , emit: versions
 
     when:
@@ -23,6 +24,15 @@ process DIAMOND_BLASTP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    switch ( outext ) {
+        case "blast": outfmt = 0; break
+        case "xml": outfmt = 5; break
+        case "txt": outfmt = 6; break
+        case "daa": outfmt = 100; break
+        case "sam": outfmt = 101; break
+        case "tsv": outfmt = 102; break
+        case "paf": outfmt = 103; break
+    }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
 
@@ -31,8 +41,9 @@ process DIAMOND_BLASTP {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
+        --outfmt ${outfmt} \\
         $args \\
-        --out ${prefix}.txt
+        --out ${prefix}.${outext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml
index 8ac1d371..1aa36c23 100644
--- a/modules/diamond/blastp/meta.yml
+++ b/modules/diamond/blastp/meta.yml
@@ -28,6 +28,14 @@ input:
       type: directory
       description: Directory containing the protein blast database
       pattern: "*"
+  - outext:
+      type: string
+      description: |
+        Specify the type of output file to be generated. `blast` corresponds to
+        BLAST pairwise format. `xml` corresponds to BLAST xml format.
+        `txt` corresponds to to BLAST tabular format. `tsv` corresponds to
+        taxonomic classification format.
+      pattern: "blast|xml|txt|daa|sam|tsv|paf"
 
 output:
   - txt:
@@ -41,3 +49,4 @@ output:
 
 authors:
   - "@spficklin"
+  - "@jfy133"
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index 3700bd36..6703c1e4 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -11,10 +11,11 @@ process DIAMOND_BLASTX {
 
     input:
     tuple val(meta), path(fasta)
-    path  db
+    path db
+    val outext
 
     output:
-    tuple val(meta), path('*.txt'), emit: txt
+    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
     path "versions.yml"           , emit: versions
 
     when:
@@ -23,6 +24,15 @@ process DIAMOND_BLASTX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    switch ( outext ) {
+        case "blast": outfmt = 0; break
+        case "xml": outfmt = 5; break
+        case "txt": outfmt = 6; break
+        case "daa": outfmt = 100; break
+        case "sam": outfmt = 101; break
+        case "tsv": outfmt = 102; break
+        case "paf": outfmt = 103; break
+    }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
 
@@ -31,8 +41,9 @@ process DIAMOND_BLASTX {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
+        --outfmt ${outfmt} \\
         $args \\
-        --out ${prefix}.txt
+        --out ${prefix}.${outext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml
index 7eb3d7b4..5ee2d55e 100644
--- a/modules/diamond/blastx/meta.yml
+++ b/modules/diamond/blastx/meta.yml
@@ -28,6 +28,14 @@ input:
       type: directory
       description: Directory containing the nucelotide blast database
       pattern: "*"
+  - outext:
+      type: string
+      description: |
+        Specify the type of output file to be generated. `blast` corresponds to
+        BLAST pairwise format. `xml` corresponds to BLAST xml format.
+        `txt` corresponds to to BLAST tabular format. `tsv` corresponds to
+        taxonomic classification format.
+      pattern: "blast|xml|txt|daa|sam|tsv|paf"
 
 output:
   - txt:
@@ -41,3 +49,4 @@ output:
 
 authors:
   - "@spficklin"
+  - "@jfy133"
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index 87d05bf9..5c1459d8 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -9,7 +9,18 @@ workflow test_diamond_blastp {
 
     db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    outext = 'txt'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+}
+
+workflow test_diamond_blastp_daa {
+
+    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    outext = 'daa'
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
 }
diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index 32dfacaa..5e31df1f 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -1,8 +1,23 @@
-- name: diamond blastp
-  command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastp/nextflow.config
+- name: diamond blastp test_diamond_blastp
+  command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
   tags:
     - diamond
     - diamond/blastp
   files:
-    - path: ./output/diamond/test.diamond_blastp.txt
+    - path: output/diamond/genome.fasta.dmnd
+      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
+    - path: output/diamond/test.diamond_blastp.txt
       md5sum: 3ca7f6290c1d8741c573370e6f8b4db0
+    - path: output/diamond/versions.yml
+
+- name: diamond blastp test_diamond_blastp_daa
+  command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config
+  tags:
+    - diamond
+    - diamond/blastp
+  files:
+    - path: output/diamond/genome.fasta.dmnd
+      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
+    - path: output/diamond/test.diamond_blastp.daa
+      md5sum: d4a79ad1fcb2ec69460e5a09a9468db7
+    - path: output/diamond/versions.yml
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index 77eb08ea..d6d5a77a 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,7 +9,18 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    outext = 'txt'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+}
+
+workflow test_diamond_blastx_daa {
+
+    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    outext = 'daa'
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
 }
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index fe7c6938..6a792f30 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -1,8 +1,24 @@
-- name: diamond blastx
-  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config
+- name: diamond blastx test_diamond_blastx
+  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
   tags:
     - diamond
     - diamond/blastx
   files:
-    - path: ./output/diamond/test.diamond_blastx.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/diamond/genome.fasta.dmnd
+      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
+    - path: output/diamond/test.diamond_blastx.txt
+    - path: output/diamond/versions.yml
+      md5sum: 747934f57b7c0f8901570500f206eac6
+
+- name: diamond blastx test_diamond_blastx_daa
+  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config
+  tags:
+    - diamond
+    - diamond/blastx
+  files:
+    - path: output/diamond/genome.fasta.dmnd
+      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
+    - path: output/diamond/test.diamond_blastx.daa
+      md5sum: 2a0ce0f7e01dcead828b87d5cbaccf7a
+    - path: output/diamond/versions.yml
+      md5sum: 05cbabfd500fc17e26b3d8061c5a78c3

From 7df2fae7469095b2f211f4e183cd5f7de77a2b98 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 29 Apr 2022 10:26:38 +0200
Subject: [PATCH 60/83] Clean up test data

---
 tests/modules/diamond/blastp/test.yml | 4 ----
 tests/modules/diamond/blastx/test.yml | 6 ------
 2 files changed, 10 deletions(-)

diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index 5e31df1f..cb297743 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -4,8 +4,6 @@
     - diamond
     - diamond/blastp
   files:
-    - path: output/diamond/genome.fasta.dmnd
-      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
     - path: output/diamond/test.diamond_blastp.txt
       md5sum: 3ca7f6290c1d8741c573370e6f8b4db0
     - path: output/diamond/versions.yml
@@ -16,8 +14,6 @@
     - diamond
     - diamond/blastp
   files:
-    - path: output/diamond/genome.fasta.dmnd
-      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
     - path: output/diamond/test.diamond_blastp.daa
       md5sum: d4a79ad1fcb2ec69460e5a09a9468db7
     - path: output/diamond/versions.yml
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index 6a792f30..a2d35c80 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -4,11 +4,8 @@
     - diamond
     - diamond/blastx
   files:
-    - path: output/diamond/genome.fasta.dmnd
-      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
     - path: output/diamond/test.diamond_blastx.txt
     - path: output/diamond/versions.yml
-      md5sum: 747934f57b7c0f8901570500f206eac6
 
 - name: diamond blastx test_diamond_blastx_daa
   command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config
@@ -16,9 +13,6 @@
     - diamond
     - diamond/blastx
   files:
-    - path: output/diamond/genome.fasta.dmnd
-      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
     - path: output/diamond/test.diamond_blastx.daa
       md5sum: 2a0ce0f7e01dcead828b87d5cbaccf7a
     - path: output/diamond/versions.yml
-      md5sum: 05cbabfd500fc17e26b3d8061c5a78c3

From 20ebb89ff97a2665106be9cace5ccb9aa4eed1be Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 10:52:40 +0200
Subject: [PATCH 61/83] update to long args

---
 modules/picard/addorreplacereadgroups/main.nf   | 10 +++++-----
 modules/picard/cleansam/main.nf                 |  4 ++--
 modules/picard/createsequencedictionary/main.nf |  4 ++--
 modules/picard/fixmateinformation/main.nf       |  4 ++--
 modules/picard/liftovervcf/main.nf              |  6 +++---
 modules/picard/markduplicates/main.nf           |  6 +++---
 modules/picard/mergesamfiles/main.nf            |  4 ++--
 modules/picard/sortvcf/main.nf                  |  4 ++--
 8 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf
index 55200d2e..fd102f67 100644
--- a/modules/picard/addorreplacereadgroups/main.nf
+++ b/modules/picard/addorreplacereadgroups/main.nf
@@ -38,11 +38,11 @@ process PICARD_ADDORREPLACEREADGROUPS {
         -Xmx${avail_mem}g \\
         --INPUT ${bam} \\
         --OUTPUT ${prefix}.bam \\
-        -ID ${ID} \\
-        -LB ${LIBRARY} \\
-        -PL ${PLATFORM} \\
-        -PU ${BARCODE} \\
-        -SM ${SAMPLE} \\
+        --RGID ${ID} \\
+        --RGLB ${LIBRARY} \\
+        --RGPL ${PLATFORM} \\
+        --RGPU ${BARCODE} \\
+        --RGSM ${SAMPLE} \\
         --CREATE_INDEX true
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf
index 4cd4db58..62989565 100644
--- a/modules/picard/cleansam/main.nf
+++ b/modules/picard/cleansam/main.nf
@@ -31,8 +31,8 @@ process PICARD_CLEANSAM {
         -Xmx${avail_mem}g \\
         CleanSam  \\
         ${args} \\
-        -I ${bam} \\
-        -O ${prefix}.bam
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf
index 3a8bb62a..735cc97b 100644
--- a/modules/picard/createsequencedictionary/main.nf
+++ b/modules/picard/createsequencedictionary/main.nf
@@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
         -Xmx${avail_mem}g \\
         CreateSequenceDictionary  \\
         $args \\
-        -R $fasta \\
-        -O ${prefix}.dict
+        --REFERENCE_SEQUENCE $fasta \\
+        --OUTPUT ${prefix}.dict
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf
index 1993e4fd..539b1082 100644
--- a/modules/picard/fixmateinformation/main.nf
+++ b/modules/picard/fixmateinformation/main.nf
@@ -31,8 +31,8 @@ process PICARD_FIXMATEINFORMATION {
     picard \\
         FixMateInformation \\
         -Xmx${avail_mem}g \\
-        -I ${bam} \\
-        -O ${prefix}.bam \\
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam \\
         --VALIDATION_STRINGENCY ${STRINGENCY}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf
index ea3f4cb7..c92abfeb 100644
--- a/modules/picard/liftovervcf/main.nf
+++ b/modules/picard/liftovervcf/main.nf
@@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
         -Xmx${avail_mem}g \\
         LiftoverVcf \\
         $args \\
-        -I $input_vcf \\
-        -O ${prefix}.lifted.vcf.gz \\
+        --INPUT $input_vcf \\
+        --OUTPUT ${prefix}.lifted.vcf.gz \\
         --CHAIN $chain \\
         --REJECT ${prefix}.unlifted.vcf.gz \\
-        -R $fasta
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index 58b6b88a..1565c647 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
         -Xmx${avail_mem}g \\
         MarkDuplicates \\
         $args \\
-        -I $bam \\
-        -O ${prefix}.bam \\
-        -M ${prefix}.MarkDuplicates.metrics.txt
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.bam \\
+        --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index 7b0185cd..1e32c63a 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -33,8 +33,8 @@ process PICARD_MERGESAMFILES {
             -Xmx${avail_mem}g \\
             MergeSamFiles \\
             $args \\
-            ${'INPUT='+bam_files.join(' INPUT=')} \\
-            OUTPUT=${prefix}.bam
+            ${'--INPUT '+bam_files.join(' --INPUT ')} \\
+            --OUTPUT ${prefix}.bam
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf
index 5fe0ecfd..fb8dbb79 100644
--- a/modules/picard/sortvcf/main.nf
+++ b/modules/picard/sortvcf/main.nf
@@ -22,8 +22,8 @@ process PICARD_SORTVCF {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
-    def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
+    def seq_dict = sequence_dict ? "--SEQUENCE_DICTIONARY $sequence_dict" : ""
+    def reference = reference ? "--REFERENCE_SEQUENCE $reference" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'

From 771d5a19f1cf72f663df27dd396e863193bc0f04 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 11:12:24 +0200
Subject: [PATCH 62/83] fix reference arg

---
 modules/picard/createsequencedictionary/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf
index 735cc97b..2348c496 100644
--- a/modules/picard/createsequencedictionary/main.nf
+++ b/modules/picard/createsequencedictionary/main.nf
@@ -31,7 +31,7 @@ process PICARD_CREATESEQUENCEDICTIONARY {
         -Xmx${avail_mem}g \\
         CreateSequenceDictionary  \\
         $args \\
-        --REFERENCE_SEQUENCE $fasta \\
+        --REFERENCE $fasta \\
         --OUTPUT ${prefix}.dict
 
     cat <<-END_VERSIONS > versions.yml

From 73600b03393ee2ec585bdc6bb5ff2585fc47bdda Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 14:20:15 +0200
Subject: [PATCH 63/83] Update subworkflows/nf-core/bam_qc_picard/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 subworkflows/nf-core/bam_qc_picard/main.nf | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index b8be04b2..c3a441bc 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -22,12 +22,8 @@ workflow BAM_QC_PICARD {
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
 
     if (ch_bait_interval || ch_target_interval) {
-        if (ch_bait_interval.isEmpty()) {
-            log.error("Bait interval channel is empty")
-        }
-        if (ch_target_interval.isEmpty()) {
-            log.error("Target interval channel is empty")
-        }
+        if (!ch_bait_interval) log.error("Bait interval channel is empty")
+        if (!ch_target_interval) log.error("Target interval channel is empty")
         PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
         ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics.first())
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())

From 71ccf0e207d2b034c931d2264b33f5f54abe1f59 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 14:24:19 +0200
Subject: [PATCH 64/83] Update subworkflows/nf-core/bam_qc_picard/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 subworkflows/nf-core/bam_qc_picard/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index c3a441bc..e3c890d5 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -25,7 +25,7 @@ workflow BAM_QC_PICARD {
         if (!ch_bait_interval) log.error("Bait interval channel is empty")
         if (!ch_target_interval) log.error("Target interval channel is empty")
         PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
-        ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics.first())
+        ch_coverage_metrics = PICARD_COLLECTHSMETRICS.out.metrics
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )

From 20e3767657ba1a4b87a412121321e79ca109b401 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 14:24:25 +0200
Subject: [PATCH 65/83] Update subworkflows/nf-core/bam_qc_picard/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 subworkflows/nf-core/bam_qc_picard/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index e3c890d5..5f46e065 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -30,7 +30,7 @@ workflow BAM_QC_PICARD {
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
-        ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics.first())
+        ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)
     }
 
     emit:

From 343c0ebe203e53ca9149ec473a8396836039a516 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 14:26:00 +0200
Subject: [PATCH 66/83] Update subworkflows/nf-core/bam_qc_picard/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 subworkflows/nf-core/bam_qc_picard/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 5f46e065..76709ea6 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -30,7 +30,7 @@ workflow BAM_QC_PICARD {
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
-        ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)
+        ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)
     }
 
     emit:

From 7e391c3a3bfc84b71e79077ba2569276e6fc5d2a Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 14:26:06 +0200
Subject: [PATCH 67/83] Update subworkflows/nf-core/bam_qc_picard/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 subworkflows/nf-core/bam_qc_picard/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 76709ea6..e38697c3 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -25,7 +25,7 @@ workflow BAM_QC_PICARD {
         if (!ch_bait_interval) log.error("Bait interval channel is empty")
         if (!ch_target_interval) log.error("Target interval channel is empty")
         PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
-        ch_coverage_metrics = PICARD_COLLECTHSMETRICS.out.metrics
+        ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
         PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )

From 9d0f03d96a6855af87f19f27728757e839e51842 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 29 Apr 2022 15:07:09 +0200
Subject: [PATCH 68/83] Update modules/elprep/merge/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/elprep/merge/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/elprep/merge/main.nf b/modules/elprep/merge/main.nf
index 28fa9985..d5ffc497 100644
--- a/modules/elprep/merge/main.nf
+++ b/modules/elprep/merge/main.nf
@@ -29,7 +29,7 @@ process ELPREP_MERGE {
     mv ${bam} input/
 
     elprep merge \\
-        input \\
+        input/ \\
         output/${prefix}.${suffix} \\
         $args \\
         ${single_end} \\

From cb29ae2187a2bc624a948eee589ad11d168a069e Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Thu, 28 Apr 2022 21:14:52 -0500
Subject: [PATCH 69/83] chore: Use forms for bug report

---
 .github/ISSUE_TEMPLATE/bug_report.md  | 64 ---------------------------
 .github/ISSUE_TEMPLATE/bug_report.yml | 50 +++++++++++++++++++++
 2 files changed, 50 insertions(+), 64 deletions(-)
 delete mode 100644 .github/ISSUE_TEMPLATE/bug_report.md
 create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
deleted file mode 100644
index f1122ea3..00000000
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ /dev/null
@@ -1,64 +0,0 @@
----
-name: Bug report
-about: Report something that is broken or incorrect
-title: "[BUG]"
----
-
-<!--
-# nf-core/module bug report
-
-Hi there!
-
-Thanks for telling us about a problem with the modules.
-Please delete this text and anything that's not relevant from the template below:
--->
-
-## Check Documentation
-
-I have checked the following places for your error:
-
-- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-- [ ] [nf-core/module documentation](https://github.com/nf-core/modules/blob/master/README.md)
-
-## Description of the bug
-
-<!-- A clear and concise description of what the bug is. -->
-
-## Steps to reproduce
-
-Steps to reproduce the behaviour:
-
-1. Command line: <!-- [e.g. `nextflow run ...`] -->
-2. See error: <!-- [Please provide your error message] -->
-
-## Expected behaviour
-
-<!-- A clear and concise description of what you expected to happen. -->
-
-## Log files
-
-Have you provided the following extra information/files:
-
-- [ ] The command used to run the module
-- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the module -->
-
-## System
-
-- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
-- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
-- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
-- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
-
-## Nextflow Installation
-
-- Version: <!-- [e.g. 19.10.0] -->
-
-## Container engine
-
-- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
-- version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. nfcore/module:2.6] -->
-
-## Additional context
-
-<!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
new file mode 100644
index 00000000..d9720fb7
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -0,0 +1,50 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/rnaseq pipeline documentation](https://nf-co.re/rnaseq/usage)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/rnaseq _(eg. 1.1, 1.5, 1.8.2)_

From 2da712f6f3d8f9b246e5fdcb1d786d5fbd6ef7d1 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Thu, 28 Apr 2022 21:29:29 -0500
Subject: [PATCH 70/83] chore: Use forms for new modules

---
 .github/ISSUE_TEMPLATE/new_module.md  | 26 -------------------
 .github/ISSUE_TEMPLATE/new_module.yml | 36 +++++++++++++++++++++++++++
 2 files changed, 36 insertions(+), 26 deletions(-)
 delete mode 100644 .github/ISSUE_TEMPLATE/new_module.md
 create mode 100644 .github/ISSUE_TEMPLATE/new_module.yml

diff --git a/.github/ISSUE_TEMPLATE/new_module.md b/.github/ISSUE_TEMPLATE/new_module.md
deleted file mode 100644
index 5c7e61cc..00000000
--- a/.github/ISSUE_TEMPLATE/new_module.md
+++ /dev/null
@@ -1,26 +0,0 @@
----
-name: New module
-about: Suggest a new module for nf-core/modules
-title: "new module: TOOL/SUBTOOL"
-label: new module
----
-
-<!--
-# nf-core/modules new module suggestion
-
-Hi there!
-
-Thanks for suggesting a new module for the modules!
-Please delete this text and anything that's not relevant from the template below:
-
-Replace TOOL with the bioconda name for the tool in the following text, so that the link is functional.
-
-Replace TOOL/SUBTOOL in the issue title so that it's understandable.
--->
-
-I think it would be good to have a module for [TOOL](https://bioconda.github.io/recipes/TOOL/README.html)
-
-- [ ] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
-- [ ] There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
-- [ ] There is no [open issue](https://github.com/nf-core/modules/issues) for this module
-- [ ] If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
diff --git a/.github/ISSUE_TEMPLATE/new_module.yml b/.github/ISSUE_TEMPLATE/new_module.yml
new file mode 100644
index 00000000..2d3e9d47
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/new_module.yml
@@ -0,0 +1,36 @@
+name: New module
+description: Suggest a new module for nf-core/modules
+title: "new module: TOOL/SUBTOOL"
+labels: new module
+body:
+  - type: checkboxes
+    attributes:
+      label: Is there an existing module for this?
+      description: This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
+      options:
+        - label: I have searched for the existing module
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Is there an open PR for this?
+      description: There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
+      options:
+        - label: I have searched for existing PRs
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Is there an open issue for this?
+      description: There is no [open issue](https://github.com/nf-core/modules/issues) for this module
+      options:
+        - label: I have searched for existing issues
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Are you going to work on this?
+      description: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
+      options:
+        - label: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
+          required: false

From 816803dbe98bc5395e87ab51862b57d5b84b2824 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Thu, 28 Apr 2022 21:36:49 -0500
Subject: [PATCH 71/83] chore: Add checkboxes for bug report

---
 .github/ISSUE_TEMPLATE/bug_report.yml | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index d9720fb7..22dc47d4 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -2,13 +2,15 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-  - type: markdown
+  - type: checkboxes
     attributes:
-      value: |
-        Before you post this issue, please check the documentation:
-
-        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/rnaseq pipeline documentation](https://nf-co.re/rnaseq/usage)
+      label: Have you checked the docs?
+      description: I have checked the following places for my error
+      options:
+        - label: "[nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)"
+          required: true
+        - label: "[nf-core modules documentation](https://nf-co.re/docs/contributing/modules)"
+          required: true
 
   - type: textarea
     id: description

From ef0483586a1a2fdeff3f90584b558f14302a2973 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Thu, 28 Apr 2022 21:46:36 -0500
Subject: [PATCH 72/83] chore: Use forms for feature request

---
 .github/ISSUE_TEMPLATE/feature_request.md  | 32 ----------------------
 .github/ISSUE_TEMPLATE/feature_request.yml | 32 ++++++++++++++++++++++
 2 files changed, 32 insertions(+), 32 deletions(-)
 delete mode 100644 .github/ISSUE_TEMPLATE/feature_request.md
 create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml

diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
deleted file mode 100644
index 72d6c058..00000000
--- a/.github/ISSUE_TEMPLATE/feature_request.md
+++ /dev/null
@@ -1,32 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for nf-core/modules
-title: "[FEATURE]"
----
-
-<!--
-# nf-core/modules feature request
-
-Hi there!
-
-Thanks for suggesting a new feature for the modules!
-Please delete this text and anything that's not relevant from the template below:
--->
-
-## Is your feature request related to a problem? Please describe
-
-<!-- A clear and concise description of what the problem is. -->
-
-<!-- e.g. [I'm always frustrated when ...] -->
-
-## Describe the solution you'd like
-
-<!-- A clear and concise description of what you want to happen. -->
-
-## Describe alternatives you've considered
-
-<!-- A clear and concise description of any alternative solutions or features you've considered. -->
-
-## Additional context
-
-<!-- Add any other context about the feature request here. -->
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
new file mode 100644
index 00000000..316fba90
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -0,0 +1,32 @@
+name: Feature request
+description: Suggest an idea for nf-core/modules
+labels: feature
+title: "[FEATURE]"
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Is your feature request related to a problem? Please describe
+      description: A clear and concise description of what the bug is.
+      placeholder: |
+        <!-- e.g. [I'm always frustrated when ...] -->
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Describe the solution you'd like
+      description: A clear and concise description of the solution you want to happen.
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Describe alternatives you've considered
+      description: A clear and concise description of any alternative solutions or features you've considered.
+
+  - type: textarea
+    id: additional_context
+    attributes:
+      label: Additional context
+      description: Add any other context about the feature request here.

From 8bee7d47489ae3a6652e7925a841f32b39f15609 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Fri, 29 Apr 2022 09:28:08 -0500
Subject: [PATCH 73/83] chore: Add image tag to bug report

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 .github/ISSUE_TEMPLATE/bug_report.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 22dc47d4..349dd44d 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -49,4 +49,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/rnaseq _(eg. 1.1, 1.5, 1.8.2)_
+        * Image tag: <!-- [e.g. nfcore/cellranger:2.6] -->

From fb02d6e85f95e5564ca446fe448e94db5a78d470 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Fri, 29 Apr 2022 09:30:03 -0500
Subject: [PATCH 74/83] chore: add OS version to bug report

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 .github/ISSUE_TEMPLATE/bug_report.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 349dd44d..71afc6b0 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -48,5 +48,5 @@ body:
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
-        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * OS and version: _(eg. CentOS Linux, macOS, Ubuntu 22.04)_
         * Image tag: <!-- [e.g. nfcore/cellranger:2.6] -->

From a8a4d76a65af792ca5ab254e9eb0cb521a70047b Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Fri, 29 Apr 2022 09:30:45 -0500
Subject: [PATCH 75/83] chore: Add container version

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 .github/ISSUE_TEMPLATE/bug_report.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
index 71afc6b0..74907cfe 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.yml
+++ b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -47,6 +47,6 @@ body:
         * Nextflow version _(eg. 21.10.3)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine and version: _(e.g. Docker 1.0.0, Singularity, Conda, Podman, Shifter or Charliecloud)_
         * OS and version: _(eg. CentOS Linux, macOS, Ubuntu 22.04)_
         * Image tag: <!-- [e.g. nfcore/cellranger:2.6] -->

From 39530b5ca710e028fdec94a704e5eed3f78c5800 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 29 Apr 2022 21:05:12 +0200
Subject: [PATCH 76/83] Bump DIAMOND version to 2.0.15

---
 modules/diamond/blastp/main.nf        | 8 +++-----
 modules/diamond/blastx/main.nf        | 8 +++-----
 modules/diamond/makedb/main.nf        | 8 +++-----
 tests/config/test_data.config         | 1 +
 tests/modules/diamond/blastp/main.nf  | 8 ++++----
 tests/modules/diamond/blastp/test.yml | 8 ++++----
 tests/modules/diamond/blastx/main.nf  | 4 ++--
 tests/modules/diamond/blastx/test.yml | 3 ++-
 tests/modules/diamond/makedb/main.nf  | 2 +-
 tests/modules/diamond/makedb/test.yml | 9 +++++----
 10 files changed, 28 insertions(+), 31 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index d7c53d6f..ccd455f4 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -2,12 +2,10 @@ process DIAMOND_BLASTP {
     tag "$meta.id"
     label 'process_medium'
 
-    // Dimaond is limited to v2.0.9 because there is not a
-    // singularity version higher than this at the current time.
-    conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
+    conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
-        'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
+        'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
+        'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index 6703c1e4..357427eb 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -2,12 +2,10 @@ process DIAMOND_BLASTX {
     tag "$meta.id"
     label 'process_medium'
 
-    // Dimaond is limited to v2.0.9 because there is not a
-    // singularity version higher than this at the current time.
-    conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
+    conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
-        'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
+        'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
+        'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/diamond/makedb/main.nf b/modules/diamond/makedb/main.nf
index e3d62f00..a76a94e5 100644
--- a/modules/diamond/makedb/main.nf
+++ b/modules/diamond/makedb/main.nf
@@ -2,12 +2,10 @@ process DIAMOND_MAKEDB {
     tag "$fasta"
     label 'process_medium'
 
-    // Dimaond is limited to v2.0.9 because there is not a
-    // singularity version higher than this at the current time.
-    conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
+    conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
-        'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
+        'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
+        'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
 
     input:
     path fasta
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 5d5535c4..62e38c4d 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -14,6 +14,7 @@ params {
                 genome_paf                                     = "${test_data_dir}/genomics/sarscov2/genome/genome.paf"
                 genome_sizes                                   = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
                 transcriptome_fasta                            = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
+                proteome_fasta                                 = "${test_data_dir}/genomics/sarscov2/genome/proteome.fasta"
                 transcriptome_paf                              = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
 
                 test_bed                                       = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index 5c1459d8..80ea2ec5 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -7,8 +7,8 @@ include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf'
 
 workflow test_diamond_blastp {
 
-    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     outext = 'txt'
 
     DIAMOND_MAKEDB ( db )
@@ -17,8 +17,8 @@ workflow test_diamond_blastp {
 
 workflow test_diamond_blastp_daa {
 
-    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     outext = 'daa'
 
     DIAMOND_MAKEDB ( db )
diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index cb297743..c2b8b6f5 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -1,19 +1,19 @@
 - name: diamond blastp test_diamond_blastp
   command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
   tags:
-    - diamond
     - diamond/blastp
+    - diamond
   files:
     - path: output/diamond/test.diamond_blastp.txt
-      md5sum: 3ca7f6290c1d8741c573370e6f8b4db0
+      md5sum: 2515cf88590afa32356497e79a51fce9
     - path: output/diamond/versions.yml
 
 - name: diamond blastp test_diamond_blastp_daa
   command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config
   tags:
-    - diamond
     - diamond/blastp
+    - diamond
   files:
     - path: output/diamond/test.diamond_blastp.daa
-      md5sum: d4a79ad1fcb2ec69460e5a09a9468db7
+      md5sum: 0b539c68a5b66dd6e20ad5d218f4f4c6
     - path: output/diamond/versions.yml
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index d6d5a77a..d5949762 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -7,7 +7,7 @@ include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
 
 workflow test_diamond_blastx {
 
-    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
     outext = 'txt'
 
@@ -17,7 +17,7 @@ workflow test_diamond_blastx {
 
 workflow test_diamond_blastx_daa {
 
-    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
     outext = 'daa'
 
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index a2d35c80..9c30ba25 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -5,6 +5,7 @@
     - diamond/blastx
   files:
     - path: output/diamond/test.diamond_blastx.txt
+      md5sum: eb2aebfa1cb42fcb2121c65528663307
     - path: output/diamond/versions.yml
 
 - name: diamond blastx test_diamond_blastx_daa
@@ -14,5 +15,5 @@
     - diamond/blastx
   files:
     - path: output/diamond/test.diamond_blastx.daa
-      md5sum: 2a0ce0f7e01dcead828b87d5cbaccf7a
+      md5sum: 0df4a833408416f32981415873facc11
     - path: output/diamond/versions.yml
diff --git a/tests/modules/diamond/makedb/main.nf b/tests/modules/diamond/makedb/main.nf
index 70982ae9..d309de6d 100644
--- a/tests/modules/diamond/makedb/main.nf
+++ b/tests/modules/diamond/makedb/main.nf
@@ -6,7 +6,7 @@ include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
 
 workflow test_diamond_makedb {
 
-    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    input = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
 
     DIAMOND_MAKEDB ( input )
 }
diff --git a/tests/modules/diamond/makedb/test.yml b/tests/modules/diamond/makedb/test.yml
index c8f2d79e..cdddf735 100644
--- a/tests/modules/diamond/makedb/test.yml
+++ b/tests/modules/diamond/makedb/test.yml
@@ -1,8 +1,9 @@
 - name: diamond makedb test_diamond_makedb
-  command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config -c ./tests/modules/diamond/makedb/nextflow.config
+  command: nextflow run tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config
   tags:
-    - diamond
     - diamond/makedb
+    - diamond
   files:
-    - path: output/diamond/genome.fasta.dmnd
-      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
+    - path: output/diamond/proteome.fasta.dmnd
+      md5sum: fc28c50b202dd7a7c5451cddff2ba1f4
+    - path: output/diamond/versions.yml

From 996385fb0f2018d4bb79bc82aea329a58a1e6fe3 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 09:36:34 +0200
Subject: [PATCH 77/83] Remove MD5sumfor DIAMOND DAA file due to occasioanlly
 variability

---
 tests/modules/diamond/blastp/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index c2b8b6f5..4fad0cbf 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -15,5 +15,4 @@
     - diamond
   files:
     - path: output/diamond/test.diamond_blastp.daa
-      md5sum: 0b539c68a5b66dd6e20ad5d218f4f4c6
     - path: output/diamond/versions.yml

From 0511e7fbbfa4ba41940d33b687b1cc90227b4eb8 Mon Sep 17 00:00:00 2001
From: Praveen <pravee1216@gmail.com>
Date: Mon, 2 May 2022 11:35:15 +0200
Subject: [PATCH 78/83] Changed BAI as optional output to handle large genome

---
 modules/gatk4/markduplicates/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf
index e8a98156..2650925b 100644
--- a/modules/gatk4/markduplicates/main.nf
+++ b/modules/gatk4/markduplicates/main.nf
@@ -12,7 +12,7 @@ process GATK4_MARKDUPLICATES {
 
     output:
     tuple val(meta), path("*.bam")    , emit: bam
-    tuple val(meta), path("*.bai")    , emit: bai
+    tuple val(meta), path("*.bai")    , optional:true, emit: bai
     tuple val(meta), path("*.metrics"), emit: metrics
     path "versions.yml"               , emit: versions
 

From 6986975bc0425e0b0e6c93dce648167f91f7ebc9 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 11:39:07 +0200
Subject: [PATCH 79/83] Fix output channels allow BLAST table customisation

---
 modules/diamond/blastp/main.nf       | 14 +++++++++---
 modules/diamond/blastp/meta.yml      | 34 ++++++++++++++++++++++++++--
 modules/diamond/blastx/main.nf       | 14 +++++++++---
 modules/diamond/blastx/meta.yml      | 28 +++++++++++++++++++++--
 tests/modules/diamond/blastp/main.nf |  6 +++--
 tests/modules/diamond/blastx/main.nf |  6 +++--
 6 files changed, 88 insertions(+), 14 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index ccd455f4..6b750145 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -11,10 +11,17 @@ process DIAMOND_BLASTP {
     tuple val(meta), path(fasta)
     path db
     val outext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
+    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
+    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
+    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
+    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
+    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
+    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,6 +29,7 @@ process DIAMOND_BLASTP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def columns = blast_columns ? "${blast_columns}" : ''
     switch ( outext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
@@ -39,7 +47,7 @@ process DIAMOND_BLASTP {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
-        --outfmt ${outfmt} \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
         --out ${prefix}.${outext}
 
diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml
index 1aa36c23..0bc12889 100644
--- a/modules/diamond/blastp/meta.yml
+++ b/modules/diamond/blastp/meta.yml
@@ -36,12 +36,42 @@ input:
         `txt` corresponds to to BLAST tabular format. `tsv` corresponds to
         taxonomic classification format.
       pattern: "blast|xml|txt|daa|sam|tsv|paf"
+  - blast_columns:
+      type: string
+      description: |
+        Optional space separated list of DIAMOND tabular BLAST output keywords
+        used for in conjunction with the 'txt' outext option (--outfmt 6). See
+        DIAMOND documnetation for more information.
 
 output:
-  - txt:
+  - blast:
       type: file
       description: File containing blastp hits
-      pattern: "*.{blastp.txt}"
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
+  - txt:
+      type: file
+      description: File containing hits in tabular BLAST format.
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index 357427eb..bb630e32 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -11,10 +11,17 @@ process DIAMOND_BLASTX {
     tuple val(meta), path(fasta)
     path db
     val outext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
+    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
+    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
+    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
+    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
+    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
+    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,6 +29,7 @@ process DIAMOND_BLASTX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def columns = blast_columns ? "${blast_columns}" : ''
     switch ( outext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
@@ -39,7 +47,7 @@ process DIAMOND_BLASTX {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
-        --outfmt ${outfmt} \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
         --out ${prefix}.${outext}
 
diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml
index 5ee2d55e..64645d34 100644
--- a/modules/diamond/blastx/meta.yml
+++ b/modules/diamond/blastx/meta.yml
@@ -38,10 +38,34 @@ input:
       pattern: "blast|xml|txt|daa|sam|tsv|paf"
 
 output:
+  - blast:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
   - txt:
       type: file
-      description: File containing blastx hits
-      pattern: "*.{blastx.txt}"
+      description: File containing hits in tabular BLAST format.
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index 80ea2ec5..e90599f0 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -10,9 +10,10 @@ workflow test_diamond_blastp {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     outext = 'txt'
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }
 
 workflow test_diamond_blastp_daa {
@@ -20,7 +21,8 @@ workflow test_diamond_blastp_daa {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     outext = 'daa'
+    blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index d5949762..8f244528 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -10,9 +10,10 @@ workflow test_diamond_blastx {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
     outext = 'txt'
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }
 
 workflow test_diamond_blastx_daa {
@@ -20,7 +21,8 @@ workflow test_diamond_blastx_daa {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
     outext = 'daa'
+    blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }

From 58e5c6aecefbff55b8f29bb542b908da0bd293f7 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 11:55:43 +0200
Subject: [PATCH 80/83] Make variables consistent

---
 modules/diamond/blastp/main.nf       | 6 +++---
 modules/diamond/blastp/meta.yml      | 4 ++--
 modules/diamond/blastx/main.nf       | 6 +++---
 modules/diamond/blastx/meta.yml      | 2 +-
 tests/modules/diamond/blastp/main.nf | 8 ++++----
 tests/modules/diamond/blastx/main.nf | 8 ++++----
 6 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index 6b750145..0d78e230 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -10,7 +10,7 @@ process DIAMOND_BLASTP {
     input:
     tuple val(meta), path(fasta)
     path db
-    val outext
+    val out_ext
     val blast_columns
 
     output:
@@ -30,7 +30,7 @@ process DIAMOND_BLASTP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def columns = blast_columns ? "${blast_columns}" : ''
-    switch ( outext ) {
+    switch ( out_ext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
         case "txt": outfmt = 6; break
@@ -49,7 +49,7 @@ process DIAMOND_BLASTP {
         --query $fasta \\
         --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${outext}
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml
index 0bc12889..3aa81e53 100644
--- a/modules/diamond/blastp/meta.yml
+++ b/modules/diamond/blastp/meta.yml
@@ -28,7 +28,7 @@ input:
       type: directory
       description: Directory containing the protein blast database
       pattern: "*"
-  - outext:
+  - out_ext:
       type: string
       description: |
         Specify the type of output file to be generated. `blast` corresponds to
@@ -40,7 +40,7 @@ input:
       type: string
       description: |
         Optional space separated list of DIAMOND tabular BLAST output keywords
-        used for in conjunction with the 'txt' outext option (--outfmt 6). See
+        used for in conjunction with the 'txt' out_ext option (--outfmt 6). See
         DIAMOND documnetation for more information.
 
 output:
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index bb630e32..ef641435 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -10,7 +10,7 @@ process DIAMOND_BLASTX {
     input:
     tuple val(meta), path(fasta)
     path db
-    val outext
+    val out_ext
     val blast_columns
 
     output:
@@ -30,7 +30,7 @@ process DIAMOND_BLASTX {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def columns = blast_columns ? "${blast_columns}" : ''
-    switch ( outext ) {
+    switch ( out_ext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
         case "txt": outfmt = 6; break
@@ -49,7 +49,7 @@ process DIAMOND_BLASTX {
         --query $fasta \\
         --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${outext}
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml
index 64645d34..2dcd7bc6 100644
--- a/modules/diamond/blastx/meta.yml
+++ b/modules/diamond/blastx/meta.yml
@@ -28,7 +28,7 @@ input:
       type: directory
       description: Directory containing the nucelotide blast database
       pattern: "*"
-  - outext:
+  - out_ext:
       type: string
       description: |
         Specify the type of output file to be generated. `blast` corresponds to
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index e90599f0..ff669233 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -9,20 +9,20 @@ workflow test_diamond_blastp {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    outext = 'txt'
+    out_ext = 'txt'
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
 
 workflow test_diamond_blastp_daa {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    outext = 'daa'
+    out_ext = 'daa'
     blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index 8f244528..bb1b55a8 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,20 +9,20 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    outext = 'txt'
+    out_ext = 'txt'
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
 
 workflow test_diamond_blastx_daa {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    outext = 'daa'
+    out_ext = 'daa'
     blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }

From 67b074382e418de8b86409af7d4b7663f6912a02 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 12:29:00 +0200
Subject: [PATCH 81/83] Fix tests

---
 modules/diamond/blastp/main.nf        | 14 +++++++-------
 modules/diamond/blastx/main.nf        | 14 +++++++-------
 tests/modules/diamond/blastp/test.yml |  1 -
 tests/modules/diamond/blastx/test.yml |  1 -
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index 0d78e230..fc77ee7b 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -14,13 +14,13 @@ process DIAMOND_BLASTP {
     val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
-    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
-    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
-    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
-    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
-    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
-    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
     path "versions.yml"               , emit: versions
 
     when:
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index ef641435..3479eedb 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -14,13 +14,13 @@ process DIAMOND_BLASTX {
     val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
-    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
-    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
-    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
-    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
-    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
-    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
     path "versions.yml"                               , emit: versions
 
     when:
diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index 4fad0cbf..aff4e1c5 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -5,7 +5,6 @@
     - diamond
   files:
     - path: output/diamond/test.diamond_blastp.txt
-      md5sum: 2515cf88590afa32356497e79a51fce9
     - path: output/diamond/versions.yml
 
 - name: diamond blastp test_diamond_blastp_daa
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index 9c30ba25..b2b6149f 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -5,7 +5,6 @@
     - diamond/blastx
   files:
     - path: output/diamond/test.diamond_blastx.txt
-      md5sum: eb2aebfa1cb42fcb2121c65528663307
     - path: output/diamond/versions.yml
 
 - name: diamond blastx test_diamond_blastx_daa

From bd3bfe0817246082525ab93707976676b1fe208b Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 12:41:24 +0200
Subject: [PATCH 82/83] Add warn of default being used

---
 modules/diamond/blastp/main.nf       | 5 +++++
 modules/diamond/blastx/main.nf       | 5 +++++
 tests/modules/diamond/blastx/main.nf | 2 +-
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index fc77ee7b..033186ea 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -38,6 +38,11 @@ process DIAMOND_BLASTP {
         case "sam": outfmt = 101; break
         case "tsv": outfmt = 102; break
         case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
     }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index 3479eedb..d3272279 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -38,6 +38,11 @@ process DIAMOND_BLASTX {
         case "sam": outfmt = 101; break
         case "tsv": outfmt = 102; break
         case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
     }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index bb1b55a8..847a64b1 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,7 +9,7 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    out_ext = 'txt'
+    out_ext = 'tfdfdt'
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )

From f1c2f624ebf8fb4368b6d5f26ea5b3cfafadf25c Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 2 May 2022 13:17:22 +0200
Subject: [PATCH 83/83] Update tests/modules/diamond/blastx/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
---
 tests/modules/diamond/blastx/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index 847a64b1..8316aa91 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,7 +9,7 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    out_ext = 'tfdfdt'
+    out_ext = 'tfdfdt'  // Nonsense file extension to check default case.
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )