From 9446428976cef86d2cd5d746adb4a08fed4e3ba0 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Tue, 29 Mar 2022 19:01:01 +0200
Subject: [PATCH 1/8] Fix typo

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

diff --git a/modules/controlfreec/freec/main.nf b/modules/controlfreec/freec/main.nf
index ba48ea1e..eb66eeaa 100644
--- a/modules/controlfreec/freec/main.nf
+++ b/modules/controlfreec/freec/main.nf
@@ -41,7 +41,7 @@ process CONTROLFREEC_FREEC {
     def chr_length                  = fai                                                       ? "chrLenFile = \${PWD}/${fai}"                                                                 : ""
     def breakpointthreshold         = task.ext.args?["general"]?["breakpointthreshold"]         ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}"                    : ""
     def breakpointtype              = task.ext.args?["general"]?["breakpointtype"]              ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}"                              : ""
-    def coefficientofvariation      = task.ext.args?["general"]?["coefficient"]                 ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}"              : ""
+    def coefficientofvariation      = task.ext.args?["general"]?["coefficientofvariation"]      ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}"              : ""
     def contamination               = task.ext.args?["general"]?["contamination"]               ? "contamination = ${task.ext.args["general"]["contamination"]}"                                : ""
     def contaminationadjustment     = task.ext.args?["general"]?["contaminationadjustment"]     ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}"            : ""
     def degree                      = task.ext.args?["general"]?["degree"]                      ? "degree = ${task.ext.args["general"]["degree"]}"                                              : ""

From 129f57ccd9adc9016aaa3f2e2e6ab556ba8de7b6 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Mon, 9 May 2022 08:50:28 +0000
Subject: [PATCH 2/8] Add meryl histogram

---
 modules/meryl/histogram/main.nf               | 34 +++++++++++++++
 modules/meryl/histogram/meta.yml              | 41 +++++++++++++++++++
 tests/config/pytest_modules.yml               | 12 ++++--
 tests/modules/meryl/histogram/main.nf         | 17 ++++++++
 tests/modules/meryl/histogram/nextflow.config |  5 +++
 tests/modules/meryl/histogram/test.yml        | 14 +++++++
 6 files changed, 119 insertions(+), 4 deletions(-)
 create mode 100644 modules/meryl/histogram/main.nf
 create mode 100644 modules/meryl/histogram/meta.yml
 create mode 100644 tests/modules/meryl/histogram/main.nf
 create mode 100644 tests/modules/meryl/histogram/nextflow.config
 create mode 100644 tests/modules/meryl/histogram/test.yml

diff --git a/modules/meryl/histogram/main.nf b/modules/meryl/histogram/main.nf
new file mode 100644
index 00000000..a1f18f05
--- /dev/null
+++ b/modules/meryl/histogram/main.nf
@@ -0,0 +1,34 @@
+process MERYL_HISTOGRAM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
+        'quay.io/biocontainers/meryl:1.3--h87f3376_1' }"
+
+    input:
+    tuple val(meta), path(meryl_db)
+
+    output:
+    tuple val(meta), path("*.hist"), emit: hist
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    meryl histogram \\
+        threads=$task.cpus \\
+        $args \\
+        $meryl_db > ${prefix}.hist
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        meryl: \$( meryl --version |& sed 's/meryl //' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/meryl/histogram/meta.yml b/modules/meryl/histogram/meta.yml
new file mode 100644
index 00000000..b786e076
--- /dev/null
+++ b/modules/meryl/histogram/meta.yml
@@ -0,0 +1,41 @@
+name: "meryl_histogram"
+description: A genomic k-mer counter (and sequence utility) with nice features.
+keywords:
+  - k-mer
+  - histogram
+tools:
+  - "meryl":
+      description: "A genomic k-mer counter (and sequence utility) with nice features. "
+      homepage: "https://github.com/marbl/meryl"
+      documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
+      tool_dev_url: "https://github.com/marbl/meryl"
+      doi: ""
+      licence: "['GPL']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - meryl_dbs:
+      type: directory
+      description: Meryl k-mer database
+
+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"
+  - hist:
+      type: file
+      description: Histogram of k-mers
+      pattern: "*.hist"
+
+authors:
+  - "@mahesh-panchal"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index b9c67363..2aa9a20d 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1214,6 +1214,10 @@ meningotype:
   - modules/meningotype/**
   - tests/modules/meningotype/**
 
+meryl/histogram:
+  - modules/meryl/histogram/**
+  - tests/modules/meryl/histogram/**
+
 metabat2/jgisummarizebamcontigdepths:
   - modules/metabat2/jgisummarizebamcontigdepths/**
   - tests/modules/metabat2/jgisummarizebamcontigdepths/**
@@ -1763,14 +1767,14 @@ slimfastq:
   - modules/slimfastq/**
   - tests/modules/slimfastq/**
 
-snapaligner/index:
-  - modules/snapaligner/index/**
-  - tests/modules/snapaligner/index/**
-
 snapaligner/align:
   - modules/snapaligner/align/**
   - tests/modules/snapaligner/align/**
 
+snapaligner/index:
+  - modules/snapaligner/index/**
+  - tests/modules/snapaligner/index/**
+
 snpdists:
   - modules/snpdists/**
   - tests/modules/snpdists/**
diff --git a/tests/modules/meryl/histogram/main.nf b/tests/modules/meryl/histogram/main.nf
new file mode 100644
index 00000000..697a12ef
--- /dev/null
+++ b/tests/modules/meryl/histogram/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MERYL_COUNT     } from '../../../../modules/meryl/count/main.nf'
+include { MERYL_HISTOGRAM } from '../../../../modules/meryl/histogram/main.nf'
+
+workflow test_meryl_histogram {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    MERYL_COUNT ( input )
+    MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
+}
diff --git a/tests/modules/meryl/histogram/nextflow.config b/tests/modules/meryl/histogram/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/meryl/histogram/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/meryl/histogram/test.yml b/tests/modules/meryl/histogram/test.yml
new file mode 100644
index 00000000..ef358943
--- /dev/null
+++ b/tests/modules/meryl/histogram/test.yml
@@ -0,0 +1,14 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml meryl/histogram
+- name: "meryl histogram"
+  command: nextflow run ./tests/modules/meryl/histogram -entry test_meryl_histogram -c ./tests/config/nextflow.config -c ./tests/modules/meryl/histogram/nextflow.config
+  tags:
+    - "meryl"
+    #
+    - "meryl/histogram"
+    #
+  files:
+    - path: "output/meryl/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/meryl/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b

From ef5f145342cb0f25be6867f9ac17fe460b11571c Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 9 May 2022 15:22:54 +0200
Subject: [PATCH 3/8] Generalize Bam2Cram do either conversion

---
 .../samtools/{bamtocram => convert}/main.nf   | 20 ++++++++----
 .../samtools/{bamtocram => convert}/meta.yml  | 12 +++----
 tests/config/pytest_modules.yml               |  6 ++--
 tests/modules/samtools/bamtocram/main.nf      | 17 ----------
 .../samtools/bamtocram/nextflow.config        |  5 ---
 tests/modules/samtools/bamtocram/test.yml     |  9 ------
 tests/modules/samtools/convert/main.nf        | 31 +++++++++++++++++++
 .../modules/samtools/convert/nextflow.config  | 12 +++++++
 tests/modules/samtools/convert/test.yml       | 21 +++++++++++++
 9 files changed, 87 insertions(+), 46 deletions(-)
 rename modules/samtools/{bamtocram => convert}/main.nf (59%)
 rename modules/samtools/{bamtocram => convert}/meta.yml (84%)
 delete mode 100644 tests/modules/samtools/bamtocram/main.nf
 delete mode 100644 tests/modules/samtools/bamtocram/nextflow.config
 delete mode 100644 tests/modules/samtools/bamtocram/test.yml
 create mode 100644 tests/modules/samtools/convert/main.nf
 create mode 100644 tests/modules/samtools/convert/nextflow.config
 create mode 100644 tests/modules/samtools/convert/test.yml

diff --git a/modules/samtools/bamtocram/main.nf b/modules/samtools/convert/main.nf
similarity index 59%
rename from modules/samtools/bamtocram/main.nf
rename to modules/samtools/convert/main.nf
index b49c308f..a7ec1bda 100644
--- a/modules/samtools/bamtocram/main.nf
+++ b/modules/samtools/convert/main.nf
@@ -1,5 +1,4 @@
-//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
-process SAMTOOLS_BAMTOCRAM {
+process SAMTOOLS_CONVERT {
     tag "$meta.id"
     label 'process_medium'
 
@@ -14,8 +13,9 @@ process SAMTOOLS_BAMTOCRAM {
     path  fai
 
     output:
-    tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
-    path  "versions.yml"                           , emit: versions
+    tuple val(meta), path("*.cram"), path("*.crai") , emit: cram_crai, optional: true
+    tuple val(meta), path("*.bam"), path("*.bai")   , emit: bam_bai, optional:true
+    path  "versions.yml"                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,9 +23,17 @@ process SAMTOOLS_BAMTOCRAM {
     script:
     def args = task.ext.args  ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def file_type = input.getExtension() == "bam" ? "cram" : "bam"
+
     """
-    samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
-    samtools index -@${task.cpus} ${prefix}.cram
+    samtools view \\
+        --threads ${task.cpus} \\
+        --reference ${fasta} \\
+        $args \\
+        $input \\
+        -o ${prefix}.${file_type}
+
+    samtools index -@${task.cpus} ${prefix}.${file_type}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/samtools/bamtocram/meta.yml b/modules/samtools/convert/meta.yml
similarity index 84%
rename from modules/samtools/bamtocram/meta.yml
rename to modules/samtools/convert/meta.yml
index 037704c6..506febb6 100644
--- a/modules/samtools/bamtocram/meta.yml
+++ b/modules/samtools/convert/meta.yml
@@ -1,5 +1,5 @@
-name: samtools_bamtocram
-description: filter/convert and then index CRAM file
+name: samtools_convert
+description: convert and then index CRAM -> BAM or BAM -> CRAM file
 keywords:
   - view
   - index
@@ -23,12 +23,12 @@ input:
         e.g. [ id:'test', single_end:false ]
   - input:
       type: file
-      description: BAM/SAM file
-      pattern: "*.{bam,sam}"
+      description: BAM/CRAM file
+      pattern: "*.{bam,cram}"
   - index:
       type: file
-      description: BAM/SAM index file
-      pattern: "*.{bai,sai}"
+      description: BAM/CRAM index file
+      pattern: "*.{bai,crai}"
   - fasta:
       type: file
       description: Reference file to create the CRAM file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index ec7fc321..53aa44b9 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1631,9 +1631,9 @@ samtools/bam2fq:
   - modules/samtools/bam2fq/**
   - tests/modules/samtools/bam2fq/**
 
-samtools/bamtocram:
-  - modules/samtools/bamtocram/**
-  - tests/modules/samtools/bamtocram/**
+samtools/convert:
+  - modules/samtools/convert/**
+  - tests/modules/samtools/convert/**
 
 samtools/collatefastq:
   - modules/samtools/collatefastq/**
diff --git a/tests/modules/samtools/bamtocram/main.nf b/tests/modules/samtools/bamtocram/main.nf
deleted file mode 100644
index b1743310..00000000
--- a/tests/modules/samtools/bamtocram/main.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/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
deleted file mode 100644
index 8730f1c4..00000000
--- a/tests/modules/samtools/bamtocram/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-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
deleted file mode 100644
index 3cb82902..00000000
--- a/tests/modules/samtools/bamtocram/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- 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
diff --git a/tests/modules/samtools/convert/main.nf b/tests/modules/samtools/convert/main.nf
new file mode 100644
index 00000000..01bdfe7f
--- /dev/null
+++ b/tests/modules/samtools/convert/main.nf
@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/convert/main.nf'
+include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/samtools/convert/main.nf'
+
+workflow test_samtools_convert_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 )
+}
+
+workflow test_samtools_convert_cramtobam {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    SAMTOOLS_CRAMTOBAM ( input, fasta, fai )
+}
diff --git a/tests/modules/samtools/convert/nextflow.config b/tests/modules/samtools/convert/nextflow.config
new file mode 100644
index 00000000..4f1e83f6
--- /dev/null
+++ b/tests/modules/samtools/convert/nextflow.config
@@ -0,0 +1,12 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName:SAMTOOLS_BAMTOCRAM{
+        ext.args = "-C"
+    }
+
+    withName:SAMTOOLS_CRAMTOBAM{
+        ext.args = "-b"
+    }
+}
diff --git a/tests/modules/samtools/convert/test.yml b/tests/modules/samtools/convert/test.yml
new file mode 100644
index 00000000..979f36ca
--- /dev/null
+++ b/tests/modules/samtools/convert/test.yml
@@ -0,0 +1,21 @@
+- name: samtools convert test_samtools_convert_bamtocram
+  command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_bamtocram -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/convert
+  files:
+    - path: output/samtools/test.cram
+    - path: output/samtools/test.cram.crai
+    - path: output/samtools/versions.yml
+
+- name: samtools convert test_samtools_convert_cramtobam
+  command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_cramtobam -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/convert
+  files:
+    - path: output/samtools/test.bam
+      md5sum: c262b6dc15f9b480bdb47d6d018b4b56
+    - path: output/samtools/test.bam.bai
+      md5sum: 6e8f5034f728401bfa841c8e70c62463
+    - path: output/samtools/versions.yml

From 24d5e7feedfe0eaefe1293f5e233c79fa63a3f9a Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 9 May 2022 15:42:55 +0200
Subject: [PATCH 4/8] Code review suggestions

---
 modules/samtools/convert/meta.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/modules/samtools/convert/meta.yml b/modules/samtools/convert/meta.yml
index 506febb6..2396f0b3 100644
--- a/modules/samtools/convert/meta.yml
+++ b/modules/samtools/convert/meta.yml
@@ -43,6 +43,10 @@ output:
       type: file
       description: filtered/converted CRAM file + index
       pattern: "*{.cram,.crai}"
+  - bam_bai:
+      type: file
+      description: filtered/converted BAM file + index
+      pattern: "*{.bam,.bai}"
   - version:
       type: file
       description: File containing software version

From da93beaf606a9f4ea7ae335ed3e25afdeac2bc26 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Mon, 9 May 2022 13:50:49 +0000
Subject: [PATCH 5/8] Update pytests

---
 tests/modules/meryl/histogram/nextflow.config |  5 +++--
 tests/modules/meryl/histogram/test.yml        | 18 +++++++-----------
 2 files changed, 10 insertions(+), 13 deletions(-)

diff --git a/tests/modules/meryl/histogram/nextflow.config b/tests/modules/meryl/histogram/nextflow.config
index 50f50a7a..6d899c50 100644
--- a/tests/modules/meryl/histogram/nextflow.config
+++ b/tests/modules/meryl/histogram/nextflow.config
@@ -1,5 +1,6 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
+    ext.args = 'k=21'
+
+}
diff --git a/tests/modules/meryl/histogram/test.yml b/tests/modules/meryl/histogram/test.yml
index ef358943..dce26b65 100644
--- a/tests/modules/meryl/histogram/test.yml
+++ b/tests/modules/meryl/histogram/test.yml
@@ -1,14 +1,10 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml meryl/histogram
-- name: "meryl histogram"
-  command: nextflow run ./tests/modules/meryl/histogram -entry test_meryl_histogram -c ./tests/config/nextflow.config -c ./tests/modules/meryl/histogram/nextflow.config
+- name: meryl histogram test_meryl_histogram
+  command: nextflow run tests/modules/meryl/histogram -entry test_meryl_histogram -c tests/config/nextflow.config
   tags:
-    - "meryl"
-    #
-    - "meryl/histogram"
-    #
+    - meryl/histogram
+    - meryl
   files:
-    - path: "output/meryl/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/meryl/test.hist
+      md5sum: 4bfdc8b287ee0cfd9922bbfa8cd64650
     - path: output/meryl/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+      md5sum: 050038f1b1df79977a393cce1b4b2ddb

From 1de1c2253e2d5c6bc37ebeda5500120f6f023750 Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 9 May 2022 16:04:58 +0200
Subject: [PATCH 6/8] Combine output after code review

---
 modules/samtools/convert/main.nf  |  7 +++----
 modules/samtools/convert/meta.yml | 10 +++-------
 2 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/modules/samtools/convert/main.nf b/modules/samtools/convert/main.nf
index a7ec1bda..b20f2b93 100644
--- a/modules/samtools/convert/main.nf
+++ b/modules/samtools/convert/main.nf
@@ -13,16 +13,15 @@ process SAMTOOLS_CONVERT {
     path  fai
 
     output:
-    tuple val(meta), path("*.cram"), path("*.crai") , emit: cram_crai, optional: true
-    tuple val(meta), path("*.bam"), path("*.bai")   , emit: bam_bai, optional:true
-    path  "versions.yml"                            , emit: versions
+    tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: aligned_index
+    path  "versions.yml"                                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args  ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def file_type = input.getExtension() == "bam" ? "cram" : "bam"
 
     """
diff --git a/modules/samtools/convert/meta.yml b/modules/samtools/convert/meta.yml
index 2396f0b3..87727255 100644
--- a/modules/samtools/convert/meta.yml
+++ b/modules/samtools/convert/meta.yml
@@ -39,14 +39,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - cram_crai:
+  - aligned_index:
       type: file
-      description: filtered/converted CRAM file + index
-      pattern: "*{.cram,.crai}"
-  - bam_bai:
-      type: file
-      description: filtered/converted BAM file + index
-      pattern: "*{.bam,.bai}"
+      description: filtered/converted BAM/CRAM file + index
+      pattern: "*{.bam/cram,.bai/crai}"
   - version:
       type: file
       description: File containing software version

From 5bd456e5e8cdc9cf8a34ce9bc5fc1f949714e0fe Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 9 May 2022 16:06:22 +0200
Subject: [PATCH 7/8] rename file_type to output extension

---
 modules/samtools/convert/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/samtools/convert/main.nf b/modules/samtools/convert/main.nf
index b20f2b93..4638d360 100644
--- a/modules/samtools/convert/main.nf
+++ b/modules/samtools/convert/main.nf
@@ -21,8 +21,8 @@ process SAMTOOLS_CONVERT {
 
     script:
     def args = task.ext.args  ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
-    def file_type = input.getExtension() == "bam" ? "cram" : "bam"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def output_extension = input.getExtension() == "bam" ? "cram" : "bam"
 
     """
     samtools view \\
@@ -30,9 +30,9 @@ process SAMTOOLS_CONVERT {
         --reference ${fasta} \\
         $args \\
         $input \\
-        -o ${prefix}.${file_type}
+        -o ${prefix}.${output_extension}
 
-    samtools index -@${task.cpus} ${prefix}.${file_type}
+    samtools index -@${task.cpus} ${prefix}.${output_extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From da79396f066a96450d9cc9f115c17c9d738595fd Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 9 May 2022 16:07:49 +0200
Subject: [PATCH 8/8] rename aligned to alignment

---
 modules/samtools/convert/main.nf  | 2 +-
 modules/samtools/convert/meta.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/samtools/convert/main.nf b/modules/samtools/convert/main.nf
index 4638d360..e0e7d725 100644
--- a/modules/samtools/convert/main.nf
+++ b/modules/samtools/convert/main.nf
@@ -13,7 +13,7 @@ process SAMTOOLS_CONVERT {
     path  fai
 
     output:
-    tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: aligned_index
+    tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index
     path  "versions.yml"                                        , emit: versions
 
     when:
diff --git a/modules/samtools/convert/meta.yml b/modules/samtools/convert/meta.yml
index 87727255..937b1403 100644
--- a/modules/samtools/convert/meta.yml
+++ b/modules/samtools/convert/meta.yml
@@ -39,7 +39,7 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - aligned_index:
+  - alignment_index:
       type: file
       description: filtered/converted BAM/CRAM file + index
       pattern: "*{.bam/cram,.bai/crai}"