From 5513d095f5240a0240cd327e3b86fa619819d3d4 Mon Sep 17 00:00:00 2001
From: Anders Sune Pedersen <aspe@clin.au.dk>
Date: Tue, 31 May 2022 15:37:26 +0200
Subject: [PATCH 01/28] Adding tbi-files to the output from GATK4_MERGEVCFS.
 #1709

---
 modules/gatk4/mergevcfs/main.nf  | 1 +
 modules/gatk4/mergevcfs/meta.yml | 6 ++++++
 2 files changed, 7 insertions(+)

diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf
index 964c1a3b..35930a6e 100644
--- a/modules/gatk4/mergevcfs/main.nf
+++ b/modules/gatk4/mergevcfs/main.nf
@@ -13,6 +13,7 @@ process GATK4_MERGEVCFS {
 
     output:
     tuple val(meta), path('*.vcf.gz'), emit: vcf
+    tuple val(meta), path("*.tbi")   , emit: tbi
     path  "versions.yml"             , emit: versions
 
     when:
diff --git a/modules/gatk4/mergevcfs/meta.yml b/modules/gatk4/mergevcfs/meta.yml
index 8d4123d9..6110e944 100644
--- a/modules/gatk4/mergevcfs/meta.yml
+++ b/modules/gatk4/mergevcfs/meta.yml
@@ -35,6 +35,12 @@ output:
       type: file
       description: merged vcf file
       pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: index files for the merged vcf files
+      pattern: "*.tbi"
+
+
   - versions:
       type: file
       description: File containing software versions

From 3e20ca7e9a0400b3d878e6c846a3b3733bfb867c Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 31 May 2022 15:46:28 +0200
Subject: [PATCH 02/28] Don't hardcode forced output names

---
 tests/modules/filtlong/nextflow.config | 1 +
 tests/modules/filtlong/test.yml        | 6 +++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/modules/filtlong/nextflow.config b/tests/modules/filtlong/nextflow.config
index ec9854c2..f0b90e67 100644
--- a/tests/modules/filtlong/nextflow.config
+++ b/tests/modules/filtlong/nextflow.config
@@ -3,5 +3,6 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     ext.args = "--min_length 10"
+    ext.prefix = "${meta.id}_lr"
 
 }
diff --git a/tests/modules/filtlong/test.yml b/tests/modules/filtlong/test.yml
index 93f847ec..87bd491b 100644
--- a/tests/modules/filtlong/test.yml
+++ b/tests/modules/filtlong/test.yml
@@ -3,7 +3,7 @@
   tags:
     - filtlong
   files:
-    - path: output/filtlong/test_lr_filtlong.fastq.gz
+    - path: output/filtlong/test_lr.fastq.gz
       contains:
         - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
@@ -12,7 +12,7 @@
   tags:
     - filtlong
   files:
-    - path: output/filtlong/test_lr_filtlong.fastq.gz
+    - path: output/filtlong/test_lr.fastq.gz
       contains:
         - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
@@ -21,6 +21,6 @@
   tags:
     - filtlong
   files:
-    - path: output/filtlong/test_lr_filtlong.fastq.gz
+    - path: output/filtlong/test_lr.fastq.gz
       contains:
         - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"

From 089f761f0bf79c4a486f1df9b6205f650196a2c1 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 31 May 2022 15:49:57 +0200
Subject: [PATCH 03/28] Actually add the changes

---
 modules/filtlong/main.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/filtlong/main.nf b/modules/filtlong/main.nf
index 67500053..9dbf05b2 100644
--- a/modules/filtlong/main.nf
+++ b/modules/filtlong/main.nf
@@ -11,7 +11,7 @@ process FILTLONG {
     tuple val(meta), path(shortreads), path(longreads)
 
     output:
-    tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
+    tuple val(meta), path("*.fastq.gz"), emit: reads
     path "versions.yml"                                     , emit: versions
 
     when:
@@ -21,12 +21,13 @@ process FILTLONG {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
+    if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     filtlong \\
         $short_reads \\
         $args \\
         $longreads \\
-        | gzip -n > ${prefix}_lr_filtlong.fastq.gz
+        | gzip -n > ${prefix}.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 98bb45cf4e93801116d9435f2c1e644f91f0628d Mon Sep 17 00:00:00 2001
From: asp8200 <aspe@clin.au.dk>
Date: Tue, 31 May 2022 13:59:56 +0000
Subject: [PATCH 04/28] Updating test for gatk4/mergevcfs

---
 tests/modules/gatk4/mergevcfs/test.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/modules/gatk4/mergevcfs/test.yml b/tests/modules/gatk4/mergevcfs/test.yml
index da2f7578..eb43a184 100644
--- a/tests/modules/gatk4/mergevcfs/test.yml
+++ b/tests/modules/gatk4/mergevcfs/test.yml
@@ -6,6 +6,8 @@
   files:
     - path: output/gatk4/test.vcf.gz
       md5sum: 5b289bda88d3a3504f2e19ee8cff177c
+    - path: output/gatk4/test.vcf.gz.tbi
+      md5sum: a81673763b13086cfce9a23e72a35a16
     - path: output/gatk4/versions.yml
 
 - name: gatk4 mergevcfs test_gatk4_mergevcfs_no_dict

From 80366924fdd0b0183cebe2258f25807db5b93c10 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 31 May 2022 16:08:13 +0200
Subject: [PATCH 05/28] added gatk4/composestrtablefile

---
 modules/gatk4/composestrtablefile/main.nf     | 51 +++++++++++++++++++
 modules/gatk4/composestrtablefile/meta.yml    | 43 ++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 .../modules/gatk4/composestrtablefile/main.nf | 16 ++++++
 .../gatk4/composestrtablefile/nextflow.config |  5 ++
 .../gatk4/composestrtablefile/test.yml        |  8 +++
 6 files changed, 127 insertions(+)
 create mode 100644 modules/gatk4/composestrtablefile/main.nf
 create mode 100644 modules/gatk4/composestrtablefile/meta.yml
 create mode 100644 tests/modules/gatk4/composestrtablefile/main.nf
 create mode 100644 tests/modules/gatk4/composestrtablefile/nextflow.config
 create mode 100644 tests/modules/gatk4/composestrtablefile/test.yml

diff --git a/modules/gatk4/composestrtablefile/main.nf b/modules/gatk4/composestrtablefile/main.nf
new file mode 100644
index 00000000..a1114f2a
--- /dev/null
+++ b/modules/gatk4/composestrtablefile/main.nf
@@ -0,0 +1,51 @@
+process GATK4_COMPOSESTRTABLEFILE {
+    tag "$fasta"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
+
+    input:
+    tuple path(fasta), path(fasta_fai), path(dict)
+
+    output:
+    path "*.zip"            , emit: str_table
+    path "versions.yml"     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    def avail_mem = 6
+    if (!task.memory) {
+        log.info '[GATK ComposeSTRTableFile] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}g" ComposeSTRTableFile \\
+        --reference $fasta \\
+        --output ${fasta.baseName}.zip \\
+        --tmp-dir . \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch test.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/gatk4/composestrtablefile/meta.yml b/modules/gatk4/composestrtablefile/meta.yml
new file mode 100644
index 00000000..eb825ef4
--- /dev/null
+++ b/modules/gatk4/composestrtablefile/meta.yml
@@ -0,0 +1,43 @@
+name: "gatk4_composestrtablefile"
+description: This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel.
+keywords:
+  - gatk4
+  - composestrtablefile
+tools:
+  - gatk4:
+      description:
+        Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/4405451249819-ComposeSTRTableFile
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ["Apache-2.0"]
+
+input:
+  - fasta:
+      type: file
+      description: FASTA reference file
+      pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: file
+      description: index of the FASTA reference file
+      pattern: "*.fai"
+  - dict:
+      type: file
+      description: Sequence dictionary of the FASTA reference file
+      pattern: "*.dict"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - str_table:
+      type: file
+      description: A zipped folder containing the STR table files
+      pattern: "*.zip"
+
+authors:
+  - "@nvnieuwk"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 3ff58b5c..bf4a6137 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -751,6 +751,10 @@ gatk4/combinegvcfs:
   - modules/gatk4/combinegvcfs/**
   - tests/modules/gatk4/combinegvcfs/**
 
+gatk4/composestrtablefile:
+  - modules/gatk4/composestrtablefile/**
+  - tests/modules/gatk4/composestrtablefile/**
+
 gatk4/createsequencedictionary:
   - modules/gatk4/createsequencedictionary/**
   - tests/modules/gatk4/createsequencedictionary/**
diff --git a/tests/modules/gatk4/composestrtablefile/main.nf b/tests/modules/gatk4/composestrtablefile/main.nf
new file mode 100644
index 00000000..9fc2e5f5
--- /dev/null
+++ b/tests/modules/gatk4/composestrtablefile/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/gatk4/composestrtablefile/main.nf'
+
+workflow test_gatk4_composestrtablefile {
+    
+    input = [
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    ]
+
+    GATK4_COMPOSESTRTABLEFILE ( input )
+}
diff --git a/tests/modules/gatk4/composestrtablefile/nextflow.config b/tests/modules/gatk4/composestrtablefile/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/gatk4/composestrtablefile/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/gatk4/composestrtablefile/test.yml b/tests/modules/gatk4/composestrtablefile/test.yml
new file mode 100644
index 00000000..3bafb348
--- /dev/null
+++ b/tests/modules/gatk4/composestrtablefile/test.yml
@@ -0,0 +1,8 @@
+- name: gatk4 composestrtablefile test_gatk4_composestrtablefile
+  command: nextflow run ./tests/modules/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/composestrtablefile/nextflow.config
+  tags:
+    - gatk4/composestrtablefile
+    - gatk4
+  files:
+    - path: output/gatk4/genome.zip
+      contains: "[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]"

From ec41ea6082fcfaadcb8a6a4f02979144de86cd91 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 31 May 2022 16:12:05 +0200
Subject: [PATCH 06/28] fix test.yml

---
 tests/modules/gatk4/composestrtablefile/test.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/modules/gatk4/composestrtablefile/test.yml b/tests/modules/gatk4/composestrtablefile/test.yml
index 3bafb348..514ae79c 100644
--- a/tests/modules/gatk4/composestrtablefile/test.yml
+++ b/tests/modules/gatk4/composestrtablefile/test.yml
@@ -1,8 +1,7 @@
 - name: gatk4 composestrtablefile test_gatk4_composestrtablefile
   command: nextflow run ./tests/modules/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/composestrtablefile/nextflow.config
   tags:
-    - gatk4/composestrtablefile
     - gatk4
+    - gatk4/composestrtablefile
   files:
-    - path: output/gatk4/genome.zip
-      contains: "[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]"
+    - path: output/gatk4/genome.zip
\ No newline at end of file

From 1166fb51505b39983af8ee16ecb382222eec22bb Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 31 May 2022 16:13:38 +0200
Subject: [PATCH 07/28] prettier

---
 tests/modules/gatk4/composestrtablefile/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/gatk4/composestrtablefile/test.yml b/tests/modules/gatk4/composestrtablefile/test.yml
index 514ae79c..597ae144 100644
--- a/tests/modules/gatk4/composestrtablefile/test.yml
+++ b/tests/modules/gatk4/composestrtablefile/test.yml
@@ -4,4 +4,4 @@
     - gatk4
     - gatk4/composestrtablefile
   files:
-    - path: output/gatk4/genome.zip
\ No newline at end of file
+    - path: output/gatk4/genome.zip

From 4199a05aeb0ec277d40cb112949bb85893310873 Mon Sep 17 00:00:00 2001
From: asp8200 <aspe@clin.au.dk>
Date: Tue, 31 May 2022 15:34:34 +0000
Subject: [PATCH 08/28] Removing redundant empty line

---
 modules/gatk4/mergevcfs/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/gatk4/mergevcfs/meta.yml b/modules/gatk4/mergevcfs/meta.yml
index 6110e944..3ebce0b9 100644
--- a/modules/gatk4/mergevcfs/meta.yml
+++ b/modules/gatk4/mergevcfs/meta.yml
@@ -40,7 +40,6 @@ output:
       description: index files for the merged vcf files
       pattern: "*.tbi"
 
-
   - versions:
       type: file
       description: File containing software versions

From df22cd80df8bee4d3f1d5750026c26c560be7392 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 31 May 2022 20:07:52 +0200
Subject: [PATCH 09/28] Fix config for tests

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

diff --git a/tests/modules/filtlong/nextflow.config b/tests/modules/filtlong/nextflow.config
index f0b90e67..5e4c9fbb 100644
--- a/tests/modules/filtlong/nextflow.config
+++ b/tests/modules/filtlong/nextflow.config
@@ -3,6 +3,6 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     ext.args = "--min_length 10"
-    ext.prefix = "${meta.id}_lr"
+    ext.prefix = "test_lr"
 
 }

From 5b74a179c3323d683065e820b2fb5a80fdaedcb7 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Wed, 1 Jun 2022 09:14:08 +0200
Subject: [PATCH 10/28] Update modules/gatk4/composestrtablefile/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 modules/gatk4/composestrtablefile/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/gatk4/composestrtablefile/main.nf b/modules/gatk4/composestrtablefile/main.nf
index a1114f2a..dae61166 100644
--- a/modules/gatk4/composestrtablefile/main.nf
+++ b/modules/gatk4/composestrtablefile/main.nf
@@ -8,7 +8,9 @@ process GATK4_COMPOSESTRTABLEFILE {
         'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
-    tuple path(fasta), path(fasta_fai), path(dict)
+   path(fasta)
+   path(fasta_fai)
+   path(dict)
 
     output:
     path "*.zip"            , emit: str_table

From d4f3df4677fb0aff66db16c896e59fc4ef93a01b Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 1 Jun 2022 09:17:05 +0200
Subject: [PATCH 11/28] Updated the test

---
 tests/modules/gatk4/composestrtablefile/main.nf  | 14 ++++++++++----
 tests/modules/gatk4/composestrtablefile/test.yml |  2 +-
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/tests/modules/gatk4/composestrtablefile/main.nf b/tests/modules/gatk4/composestrtablefile/main.nf
index 9fc2e5f5..da8967cc 100644
--- a/tests/modules/gatk4/composestrtablefile/main.nf
+++ b/tests/modules/gatk4/composestrtablefile/main.nf
@@ -6,11 +6,17 @@ include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/gatk4/composestr
 
 workflow test_gatk4_composestrtablefile {
     
-    input = [
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true),
+    fasta = [
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    fasta_fai = [
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ]
+
+    dict = [
         file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
     ]
 
-    GATK4_COMPOSESTRTABLEFILE ( input )
+    GATK4_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict )
 }
diff --git a/tests/modules/gatk4/composestrtablefile/test.yml b/tests/modules/gatk4/composestrtablefile/test.yml
index 597ae144..0a87372a 100644
--- a/tests/modules/gatk4/composestrtablefile/test.yml
+++ b/tests/modules/gatk4/composestrtablefile/test.yml
@@ -1,7 +1,7 @@
 - name: gatk4 composestrtablefile test_gatk4_composestrtablefile
   command: nextflow run ./tests/modules/gatk4/composestrtablefile -entry test_gatk4_composestrtablefile -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/composestrtablefile/nextflow.config
   tags:
-    - gatk4
     - gatk4/composestrtablefile
+    - gatk4
   files:
     - path: output/gatk4/genome.zip

From 8470f3cb7e790701401523c58a72e183ac47ecac Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 1 Jun 2022 09:20:20 +0200
Subject: [PATCH 12/28] linting

---
 tests/modules/gatk4/composestrtablefile/main.nf | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/tests/modules/gatk4/composestrtablefile/main.nf b/tests/modules/gatk4/composestrtablefile/main.nf
index da8967cc..8fccadb9 100644
--- a/tests/modules/gatk4/composestrtablefile/main.nf
+++ b/tests/modules/gatk4/composestrtablefile/main.nf
@@ -6,17 +6,11 @@ include { GATK4_COMPOSESTRTABLEFILE } from '../../../../modules/gatk4/composestr
 
 workflow test_gatk4_composestrtablefile {
     
-    fasta = [
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    fasta_fai = [
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
-    ]
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    dict = [
-        file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
-    ]
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
 
     GATK4_COMPOSESTRTABLEFILE ( fasta, fasta_fai, dict )
 }

From 114a54c8d5a8e898a126c2804e3e221286eb2682 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 1 Jun 2022 09:22:09 +0200
Subject: [PATCH 13/28] spaces fix

---
 modules/gatk4/composestrtablefile/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/gatk4/composestrtablefile/main.nf b/modules/gatk4/composestrtablefile/main.nf
index dae61166..8f2f00f2 100644
--- a/modules/gatk4/composestrtablefile/main.nf
+++ b/modules/gatk4/composestrtablefile/main.nf
@@ -8,9 +8,9 @@ process GATK4_COMPOSESTRTABLEFILE {
         'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
-   path(fasta)
-   path(fasta_fai)
-   path(dict)
+    path(fasta)
+    path(fasta_fai)
+    path(dict)
 
     output:
     path "*.zip"            , emit: str_table

From f6953b51478d24a4caf84b40d92bba3350a38507 Mon Sep 17 00:00:00 2001
From: SusiJo <susanne.jodoin@gmx.de>
Date: Wed, 1 Jun 2022 17:35:02 +0200
Subject: [PATCH 14/28] adjust cnvkit/batch for germline mode

---
 modules/cnvkit/batch/main.nf        | 38 +++++++++++------
 tests/config/test_data.config       |  6 +--
 tests/modules/cnvkit/batch/main.nf  | 22 ++++++++--
 tests/modules/cnvkit/batch/test.yml | 63 ++++++++++++++++++++++++++---
 4 files changed, 104 insertions(+), 25 deletions(-)

diff --git a/modules/cnvkit/batch/main.nf b/modules/cnvkit/batch/main.nf
index c1f9ef87..b467c6f2 100644
--- a/modules/cnvkit/batch/main.nf
+++ b/modules/cnvkit/batch/main.nf
@@ -28,34 +28,48 @@ process CNVKIT_BATCH {
     script:
     def args = task.ext.args ?: ''
 
-    // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
-    // input pair is assumed to have same extension if both exist
-    def is_cram = tumor.Extension == "cram" ? true : false
-    def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"
+    def tumor_exists = tumor ? true : false
+    def normal_exists = normal ? true : false
+
+    // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
+    def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
+    def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
+
+    def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
 
-    // do not run samtools on normal samples in tumor_only mode
-    def normal_exists = normal ? true: false
     // tumor_only mode does not need fasta & target
     // instead it requires a pre-computed reference.cnn which is built from fasta & target
     def (normal_out, normal_args, fasta_args) = ["", "", ""]
 
     if (normal_exists){
         def normal_prefix = normal.BaseName
-        normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}"
-        normal_args = normal_prefix ? "--normal $normal_out" : ""
+        normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
         fasta_args = fasta ? "--fasta $fasta" : ""
+
+        // germline mode
+        // normal samples must be input without a flag
+        // requires flag --normal to be empty
+        if(!tumor_exists){
+            tumor_out = normal.BaseName + ".bam"
+            normal_args = "--normal "
+        }
+        // somatic mode
+        else {
+            normal_args = normal_prefix ? "--normal $normal_out" : ""
+        }
     }
 
     def target_args = targets ? "--targets $targets" : ""
     def reference_args = reference ? "--reference $reference" : ""
 
     """
-    if $is_cram; then
+    if $tumor_cram; then
         samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
-        if $normal_exists; then
-            samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
-        fi
     fi
+    if $normal_cram; then
+        samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
+    fi
+
 
     cnvkit.py \\
         batch \\
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index cf7d45f6..bef6f0c9 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -23,6 +23,8 @@ params {
                 test_bed12                                     = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
                 baits_bed                                      = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
 
+                reference_cnn                                  = "${test_data_dir}/genomics/sarscov2/genome/cnn/reference.cnn"
+
                 kraken2                                        = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
                 kraken2_tar_gz                                 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
 
@@ -145,6 +147,7 @@ params {
                 genome_21_multi_interval_bed_gz                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
                 genome_21_multi_interval_bed_gz_tbi            = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
                 genome_21_chromosomes_dir                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
+                genome_21_reference_cnn                        = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn"
 
                 dbsnp_146_hg38_elsites                         = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites"
                 dbsnp_146_hg38_vcf_gz                          = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
@@ -414,9 +417,6 @@ params {
             'txt' {
                 hello                           = "${test_data_dir}/generic/txt/hello.txt"
             }
-            'cnn' {
-                reference                       = "${test_data_dir}/generic/cnn/reference.cnn"
-            }
             'cooler'{
                 test_pairix_pair_gz             = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
                 test_pairix_pair_gz_px2         = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
diff --git a/tests/modules/cnvkit/batch/main.nf b/tests/modules/cnvkit/batch/main.nf
index 988ed3ad..c93e3a00 100755
--- a/tests/modules/cnvkit/batch/main.nf
+++ b/tests/modules/cnvkit/batch/main.nf
@@ -5,6 +5,7 @@ nextflow.enable.dsl = 2
 include { CNVKIT_BATCH as CNVKIT_HYBRID    } from '../../../../modules/cnvkit/batch/main.nf'
 include { CNVKIT_BATCH as CNVKIT_WGS       } from '../../../../modules/cnvkit/batch/main.nf'
 include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
+include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
 
 workflow test_cnvkit_hybrid {
 
@@ -47,10 +48,10 @@ workflow test_cnvkit_tumoronly {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
         []
     ]
-    reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
+    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
     CNVKIT_TUMORONLY ( input, [], [], reference )
 }
@@ -59,11 +60,24 @@ workflow test_cnvkit_tumoronly_cram {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
         []
     ]
     fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
-    reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
+    reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
     CNVKIT_TUMORONLY ( input, fasta, [], reference )
 }
+
+workflow test_cnvkit_germline_cram {
+
+    input = [
+        [ id:'test'], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    CNVKIT_GERMLINE ( input, fasta, targets,  [])
+}
diff --git a/tests/modules/cnvkit/batch/test.yml b/tests/modules/cnvkit/batch/test.yml
index 00d6a767..928a08de 100755
--- a/tests/modules/cnvkit/batch/test.yml
+++ b/tests/modules/cnvkit/batch/test.yml
@@ -92,9 +92,22 @@
     - cnvkit
     - cnvkit/batch
   files:
-    - path: output/cnvkit/reference.antitarget-tmp.bed
-    - path: output/cnvkit/reference.target-tmp.bed
-      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
+    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/reference_chr21.target-tmp.bed
+      md5sum: 657b25dbda8516624efa8cb2cf3716ca
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: f7caeca04aba28b125ce26b511f42afb
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: d9bdb71ce807051369577ee7f807a40c
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 2b56aac606ba6183d018b30ca58afcec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
 
 - name: cnvkit batch test_cnvkit_tumoronly_cram
   command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
@@ -102,6 +115,44 @@
     - cnvkit
     - cnvkit/batch
   files:
-    - path: output/cnvkit/reference.antitarget-tmp.bed
-    - path: output/cnvkit/reference.target-tmp.bed
-      md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
+    - path: output/cnvkit/reference_chr21.antitarget-tmp.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/reference_chr21.target-tmp.bed
+      md5sum: 657b25dbda8516624efa8cb2cf3716ca
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: f6adc75a0a86b7a921eca1b79a394cb0
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: f7caeca04aba28b125ce26b511f42afb
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: d9bdb71ce807051369577ee7f807a40c
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 2b56aac606ba6183d018b30ca58afcec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
+
+- name: cnvkit batch test_cnvkit_germline_cram
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/multi_intervals.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/multi_intervals.target.bed
+      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
+    - path: output/cnvkit/reference.cnn
+      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: 68b62b75cd91b2ffe5633686fb943490
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: df196edd72613c59186f4d87df3dc4a4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: 3b4fc0cc73be78f978cfe2422470753e
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f

From a21cfb666eed7517060f1d2d61a21c340753b0ec Mon Sep 17 00:00:00 2001
From: SusiJo <susanne.jodoin@gmx.de>
Date: Thu, 2 Jun 2022 10:38:05 +0200
Subject: [PATCH 15/28] changed container + add cram2bam conversion

---
 modules/deeptools/bamcoverage/main.nf        | 58 +++++++++++++++-----
 modules/deeptools/bamcoverage/meta.yml       |  9 +++
 tests/modules/deeptools/bamcoverage/main.nf  | 18 +++++-
 tests/modules/deeptools/bamcoverage/test.yml | 21 ++++---
 4 files changed, 82 insertions(+), 24 deletions(-)

diff --git a/modules/deeptools/bamcoverage/main.nf b/modules/deeptools/bamcoverage/main.nf
index 926bf0ad..04073ed9 100644
--- a/modules/deeptools/bamcoverage/main.nf
+++ b/modules/deeptools/bamcoverage/main.nf
@@ -2,13 +2,15 @@ process DEEPTOOLS_BAMCOVERAGE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
+    conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
-        'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
+        'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
+    path(fasta)
+    path(fasta_fai)
 
     output:
     tuple val(meta), path("*.bigWig")   , emit: bigwig, optional: true
@@ -22,16 +24,44 @@ process DEEPTOOLS_BAMCOVERAGE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
 
-    """
-    bamCoverage \\
-        --bam $input \\
-        $args \\
-        --numberOfProcessors ${task.cpus} \\
-        --outFileName ${prefix}
+    // cram_input is currently not working with deeptools
+    // therefore it's required to convert cram to bam first
+    def is_cram = input.Extension == "cram" ? true : false
+    def input_out = is_cram ? input.BaseName + ".bam" : "${input}"
+    def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
+
+    if (is_cram){
+        """
+        samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
+        samtools index -b $input_out -@ $task.cpus
+
+        bamCoverage \\
+            --bam $input_out \\
+            $args \\
+            --numberOfProcessors ${task.cpus} \\
+            --outFileName ${prefix}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
+        END_VERSIONS
+        """
+
+    }
+    else {
+        """
+        bamCoverage \\
+            --bam $input_out \\
+            $args \\
+            --numberOfProcessors ${task.cpus} \\
+            --outFileName ${prefix}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
+        END_VERSIONS
+        """
+    }
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
-    END_VERSIONS
-    """
 }
diff --git a/modules/deeptools/bamcoverage/meta.yml b/modules/deeptools/bamcoverage/meta.yml
index fb92168f..c6566910 100644
--- a/modules/deeptools/bamcoverage/meta.yml
+++ b/modules/deeptools/bamcoverage/meta.yml
@@ -25,6 +25,14 @@ input:
       type: file
       description: BAM/CRAM index file
       pattern: "*.{bai,crai}"
+  - fasta:
+      type: file
+      description: Reference file the CRAM file was created with (required with CRAM input)
+      pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: file
+      description: Index of the reference file (optional, but recommended)
+      pattern: "*.{fai}"
 
 output:
   - meta:
@@ -47,3 +55,4 @@ output:
 
 authors:
   - "@FriederikeHanssen"
+  - "@SusiJo"
diff --git a/tests/modules/deeptools/bamcoverage/main.nf b/tests/modules/deeptools/bamcoverage/main.nf
index fb5c1c2d..97a79508 100644
--- a/tests/modules/deeptools/bamcoverage/main.nf
+++ b/tests/modules/deeptools/bamcoverage/main.nf
@@ -12,7 +12,7 @@ workflow test_deeptools_bamcoverage_bam {
           file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
         ]
 
-    DEEPTOOLS_BAMCOVERAGE ( input )
+    DEEPTOOLS_BAMCOVERAGE ( input, [], [] )
 }
 
 workflow test_deeptools_bamcoverage_cram {
@@ -22,6 +22,20 @@ workflow test_deeptools_bamcoverage_cram {
           file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
           file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
         ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    DEEPTOOLS_BAMCOVERAGE ( input )
+    DEEPTOOLS_BAMCOVERAGE ( input, fasta, fasta_fai)
+}
+
+workflow test_deeptools_bamcoverage_cram_no_fasta_fai {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+          file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+        ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    DEEPTOOLS_BAMCOVERAGE ( input, fasta, [])
 }
diff --git a/tests/modules/deeptools/bamcoverage/test.yml b/tests/modules/deeptools/bamcoverage/test.yml
index 736c2e61..63ef6442 100644
--- a/tests/modules/deeptools/bamcoverage/test.yml
+++ b/tests/modules/deeptools/bamcoverage/test.yml
@@ -1,21 +1,26 @@
 - name: deeptools bamcoverage test_deeptools_bamcoverage_bam
-  command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
   tags:
-    - deeptools
     - deeptools/bamcoverage
+    - deeptools
   files:
     - path: output/deeptools/test.bigWig
       md5sum: 95fe9383a9e6c02aea6b785cf074274f
-    - path: output/deeptools/versions.yml
-      md5sum: 68c94e73b7a8c0935578bad61fea54c1
 
 - name: deeptools bamcoverage test_deeptools_bamcoverage_cram
-  command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
   tags:
-    - deeptools
     - deeptools/bamcoverage
+    - deeptools
+  files:
+    - path: output/deeptools/test.bigWig
+      md5sum: 95fe9383a9e6c02aea6b785cf074274f
+
+- name: deeptools bamcoverage test_deeptools_bamcoverage_cram_no_fasta_fai
+  command: nextflow run ./tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram_no_fasta_fai -c ./tests/config/nextflow.config  -c ./tests/modules/deeptools/bamcoverage/nextflow.config
+  tags:
+    - deeptools/bamcoverage
+    - deeptools
   files:
     - path: output/deeptools/test.bigWig
       md5sum: 95fe9383a9e6c02aea6b785cf074274f
-    - path: output/deeptools/versions.yml
-      md5sum: 665bbd2979c49bf3974a24bd44a88e94

From 51be617b1ca9bff973655eb899d591ed6ab253b5 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 2 Jun 2022 11:09:55 +0200
Subject: [PATCH 16/28] fix untar output dir

---
 modules/untar/main.nf         |  8 +++++++-
 tests/config/test_data.config |  2 ++
 tests/modules/untar/main.nf   | 10 ++++++++++
 tests/modules/untar/test.yml  | 12 ++++++++++--
 4 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/modules/untar/main.nf b/modules/untar/main.nf
index 058d1764..29ab10a5 100644
--- a/modules/untar/main.nf
+++ b/modules/untar/main.nf
@@ -21,12 +21,18 @@ process UNTAR {
     def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     untar     = archive.toString() - '.tar.gz'
+
     """
+    mkdir output
+
     tar \\
+        -C output --strip-components 1 \\
         -xzvf \\
         $args \\
         $archive \\
-        $args2 \\
+        $args2
+
+    mv output ${untar}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 39331664..4af77d92 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -323,6 +323,8 @@ params {
                 test_sv_vcf                                   =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
 
                 test_pytor                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
+
+                test_flowcell                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz"
             }
             'pacbio' {
                 primers                         = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
diff --git a/tests/modules/untar/main.nf b/tests/modules/untar/main.nf
index 9d6d4c6c..3b7daedd 100644
--- a/tests/modules/untar/main.nf
+++ b/tests/modules/untar/main.nf
@@ -12,3 +12,13 @@ workflow test_untar {
 
     UNTAR ( input )
 }
+
+
+workflow test_untar_different_output_path {
+    input = [
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true)
+    ]
+
+    UNTAR ( input )
+}
diff --git a/tests/modules/untar/test.yml b/tests/modules/untar/test.yml
index 6d0d1d12..6599f105 100644
--- a/tests/modules/untar/test.yml
+++ b/tests/modules/untar/test.yml
@@ -1,5 +1,5 @@
-- name: untar
-  command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config -c ./tests/modules/untar/nextflow.config
+- name: untar test_untar
+  command: nextflow run ./tests/modules/untar -entry test_untar -c ./tests/config/nextflow.config  -c ./tests/modules/untar/nextflow.config
   tags:
     - untar
   files:
@@ -9,3 +9,11 @@
       md5sum: a033d00cf6759407010b21700938f543
     - path: output/untar/kraken2/taxo.k2d
       md5sum: 094d5891cdccf2f1468088855c214b2c
+
+- name: untar test_untar_different_output_path
+  command: nextflow run ./tests/modules/untar -entry test_untar_different_output_path -c ./tests/config/nextflow.config  -c ./tests/modules/untar/nextflow.config
+  tags:
+    - untar
+  files:
+    - path: output/untar/flowcell/RunInfo.xml
+      md5sum: 03038959f4dd181c86bc97ae71fe270a

From 2f3ddc90fbeda9fcf54f25b84465f5ac149d2b75 Mon Sep 17 00:00:00 2001
From: SusiJo <susanne.jodoin@gmx.de>
Date: Thu, 2 Jun 2022 12:57:50 +0200
Subject: [PATCH 17/28] added fasta_fai as input + changed if statements

---
 modules/cnvkit/batch/main.nf        | 152 +++++++++++++++++++++++-----
 modules/cnvkit/batch/meta.yml       |   4 +
 tests/modules/cnvkit/batch/main.nf  |  44 +++++---
 tests/modules/cnvkit/batch/test.yml |  49 ++++++---
 4 files changed, 200 insertions(+), 49 deletions(-)

diff --git a/modules/cnvkit/batch/main.nf b/modules/cnvkit/batch/main.nf
index b467c6f2..090f7860 100644
--- a/modules/cnvkit/batch/main.nf
+++ b/modules/cnvkit/batch/main.nf
@@ -10,6 +10,7 @@ process CNVKIT_BATCH {
     input:
     tuple val(meta), path(tumor), path(normal)
     path  fasta
+    path  fasta_fai
     path  targets
     path  reference
 
@@ -34,12 +35,15 @@ process CNVKIT_BATCH {
     // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
     def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
     def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
+    def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
+    def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
 
     def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
 
     // tumor_only mode does not need fasta & target
     // instead it requires a pre-computed reference.cnn which is built from fasta & target
     def (normal_out, normal_args, fasta_args) = ["", "", ""]
+    def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
 
     if (normal_exists){
         def normal_prefix = normal.BaseName
@@ -48,9 +52,9 @@ process CNVKIT_BATCH {
 
         // germline mode
         // normal samples must be input without a flag
-        // requires flag --normal to be empty
+        // requires flag --normal to be empty []
         if(!tumor_exists){
-            tumor_out = normal.BaseName + ".bam"
+            tumor_out = "${normal_prefix}" + ".bam"
             normal_args = "--normal "
         }
         // somatic mode
@@ -62,28 +66,130 @@ process CNVKIT_BATCH {
     def target_args = targets ? "--targets $targets" : ""
     def reference_args = reference ? "--reference $reference" : ""
 
-    """
-    if $tumor_cram; then
-        samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
-    fi
-    if $normal_cram; then
-        samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
-    fi
+    // somatic_mode cram_input
+    if (tumor_cram && normal_cram){
+        """
+        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
+        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out
 
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
 
-    cnvkit.py \\
-        batch \\
-        $tumor_out \\
-        $normal_args \\
-        $fasta_args \\
-        $reference_args \\
-        $target_args \\
-        --processes $task.cpus \\
-        $args
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // somatic_mode bam_input
+    else if (tumor_bam && normal_bam){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // tumor_only_mode cram_input
+    else if(tumor_cram && !normal_exists){
+        """
+        samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
+
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // tumor_only bam_input
+    else if(tumor_bam && !normal_exists){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // germline mode cram_input
+    // normal_args must be --normal []
+    else if (normal_cram && !tumor_exists){
+        """
+        samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out
+
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
+    // germline mode bam_input
+    else if (normal_bam && !tumor_exists){
+        """
+        cnvkit.py \\
+            batch \\
+            $tumor_out \\
+            $normal_args \\
+            $fasta_args \\
+            $reference_args \\
+            $target_args \\
+            --processes $task.cpus \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
+        END_VERSIONS
+        """
+    }
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
-    END_VERSIONS
-    """
 }
diff --git a/modules/cnvkit/batch/meta.yml b/modules/cnvkit/batch/meta.yml
index 2cd675c7..89762192 100644
--- a/modules/cnvkit/batch/meta.yml
+++ b/modules/cnvkit/batch/meta.yml
@@ -29,6 +29,10 @@ input:
       type: file
       description: |
         Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
+  - fasta_fai:
+      type: file
+      description: |
+        Input reference genome fasta index (optional, but recommended for cram_input)
   - targetfile:
       type: file
       description: |
diff --git a/tests/modules/cnvkit/batch/main.nf b/tests/modules/cnvkit/batch/main.nf
index c93e3a00..daf87a37 100755
--- a/tests/modules/cnvkit/batch/main.nf
+++ b/tests/modules/cnvkit/batch/main.nf
@@ -7,7 +7,7 @@ include { CNVKIT_BATCH as CNVKIT_WGS       } from '../../../../modules/cnvkit/ba
 include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
 include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
 
-workflow test_cnvkit_hybrid {
+workflow test_cnvkit_hybrid_somatic {
 
     input = [
         [ id:'test' ], // meta map
@@ -17,10 +17,10 @@ workflow test_cnvkit_hybrid {
     fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
 
-    CNVKIT_HYBRID ( input, fasta, targets, [] )
+    CNVKIT_HYBRID ( input, fasta, [], targets, [] )
 }
 
-workflow test_cnvkit_wgs {
+workflow test_cnvkit_wgs_somatic {
 
     input = [
         [ id:'test'], // meta map
@@ -29,22 +29,24 @@ workflow test_cnvkit_wgs {
     ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
-    CNVKIT_WGS ( input, fasta, [], [] )
+    CNVKIT_WGS ( input, fasta, [], [], [] )
 }
 
-workflow test_cnvkit_cram {
+workflow test_cnvkit_cram_wgs_somatic {
 
     input = [
         [ id:'test'], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
     ]
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai     = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
 
-    CNVKIT_WGS ( input, fasta, [], [] )
+    CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
 }
 
-workflow test_cnvkit_tumoronly {
+
+workflow test_cnvkit_tumoronly_hybrid_bam {
 
     input = [
         [ id:'test'], // meta map
@@ -53,10 +55,10 @@ workflow test_cnvkit_tumoronly {
     ]
     reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
-    CNVKIT_TUMORONLY ( input, [], [], reference )
+    CNVKIT_TUMORONLY ( input, [], [],  [], reference )
 }
 
-workflow test_cnvkit_tumoronly_cram {
+workflow test_cnvkit_tumoronly_hybrid_cram {
 
     input = [
         [ id:'test'], // meta map
@@ -66,10 +68,10 @@ workflow test_cnvkit_tumoronly_cram {
     fasta     = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
 
-    CNVKIT_TUMORONLY ( input, fasta, [], reference )
+    CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
 }
 
-workflow test_cnvkit_germline_cram {
+workflow test_cnvkit_germline_hybrid_cram {
 
     input = [
         [ id:'test'], // meta map
@@ -77,7 +79,21 @@ workflow test_cnvkit_germline_cram {
         file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
     ]
     fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
 
-    CNVKIT_GERMLINE ( input, fasta, targets,  [])
+    CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets,  [])
+}
+
+workflow test_cnvkit_germline_hybrid_bam {
+
+    input = [
+        [ id:'test'], // meta map
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
+    ]
+    fasta     = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    targets   = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    CNVKIT_GERMLINE ( input, fasta, [], targets,  [])
 }
diff --git a/tests/modules/cnvkit/batch/test.yml b/tests/modules/cnvkit/batch/test.yml
index 928a08de..006e142f 100755
--- a/tests/modules/cnvkit/batch/test.yml
+++ b/tests/modules/cnvkit/batch/test.yml
@@ -1,5 +1,5 @@
-- name: cnvkit batch test_cnvkit_hybrid
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+- name: cnvkit batch test_cnvkit_hybrid_somatic
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -26,8 +26,8 @@
     - path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
       md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
 
-- name: cnvkit batch test_cnvkit_wgs
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+- name: cnvkit batch test_cnvkit_wgs_somatic
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -56,8 +56,8 @@
     - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
       md5sum: 6ae6b3fce7299eedca6133d911c38fe1
 
-- name: cnvkit batch test_cnvkit_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+- name: cnvkit batch test_cnvkit_cram_wgs_somatic
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -86,8 +86,8 @@
     - path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
       md5sum: 6ae6b3fce7299eedca6133d911c38fe1
 
-- name: cnvkit batch test_cnvkit_tumoronly
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -109,8 +109,8 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
       md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
 
-- name: cnvkit batch test_cnvkit_tumoronly_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch
@@ -132,8 +132,33 @@
     - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
       md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
 
-- name: cnvkit batch test_cnvkit_germline_cram
-  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+- name: cnvkit batch test_cnvkit_germline_hybrid_cram
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
+  tags:
+    - cnvkit
+    - cnvkit/batch
+  files:
+    - path: output/cnvkit/multi_intervals.antitarget.bed
+      md5sum: 3d4d20f9f23b39970865d29ef239d20b
+    - path: output/cnvkit/multi_intervals.target.bed
+      md5sum: 86d30493bb2e619a93f4ebc2923d29f3
+    - path: output/cnvkit/reference.cnn
+      md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
+      md5sum: 067115082c4af4b64d58c0dc3a3642e4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
+      md5sum: 68b62b75cd91b2ffe5633686fb943490
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
+      md5sum: df196edd72613c59186f4d87df3dc4a4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
+      md5sum: 3b4fc0cc73be78f978cfe2422470753e
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
+      md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
+    - path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
+      md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
+
+- name: cnvkit batch test_cnvkit_germline_hybrid_bam
+  command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config  -c ./tests/modules/cnvkit/batch/nextflow.config
   tags:
     - cnvkit
     - cnvkit/batch

From 2a45d4286895d77d47b3a3dd9bc845b4d13276df Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 2 Jun 2022 13:17:06 +0200
Subject: [PATCH 18/28] added the calibratedragstrmodel module

---
 modules/gatk4/calibratedragstrmodel/main.nf   | 48 +++++++++++++
 modules/gatk4/calibratedragstrmodel/meta.yml  | 70 +++++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/config/test_data.config                 |  1 +
 .../gatk4/calibratedragstrmodel/main.nf       | 44 ++++++++++++
 .../calibratedragstrmodel/nextflow.config     |  5 ++
 .../gatk4/calibratedragstrmodel/test.yml      | 17 +++++
 7 files changed, 189 insertions(+)
 create mode 100644 modules/gatk4/calibratedragstrmodel/main.nf
 create mode 100644 modules/gatk4/calibratedragstrmodel/meta.yml
 create mode 100644 tests/modules/gatk4/calibratedragstrmodel/main.nf
 create mode 100644 tests/modules/gatk4/calibratedragstrmodel/nextflow.config
 create mode 100644 tests/modules/gatk4/calibratedragstrmodel/test.yml

diff --git a/modules/gatk4/calibratedragstrmodel/main.nf b/modules/gatk4/calibratedragstrmodel/main.nf
new file mode 100644
index 00000000..6682753d
--- /dev/null
+++ b/modules/gatk4/calibratedragstrmodel/main.nf
@@ -0,0 +1,48 @@
+process GATK4_CALIBRATEDRAGSTRMODEL{
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bam_index)
+    path  fasta
+    path  fasta_fai
+    path  dict
+    path  strtablefile
+
+    output:
+    tuple val(meta), path("*.txt")   , emit: dragstr_model
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK CalibrateDragstrModel] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}g" CalibrateDragstrModel \\
+        --input $bam \\
+        --output ${prefix}.txt \\
+        --reference $fasta \\
+        --str-table-path $strtablefile \\
+        --tmp-dir . \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/gatk4/calibratedragstrmodel/meta.yml b/modules/gatk4/calibratedragstrmodel/meta.yml
new file mode 100644
index 00000000..f72a4f60
--- /dev/null
+++ b/modules/gatk4/calibratedragstrmodel/meta.yml
@@ -0,0 +1,70 @@
+name: "gatk4_calibratedragstrmodel"
+description: estimates the parameters for the DRAGstr model
+keywords:
+  - gatk4
+  - bam
+  - cram
+  - sam
+  - calibratedragstrmodel
+tools:
+  - gatk4:
+      description:
+        Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360057441571-CalibrateDragstrModel-BETA-
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ["Apache-2.0"]
+
+input:
+  # Only when we have meta
+  - 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}"
+  - bam_index:
+      type: file
+      description: index of the BAM/CRAM/SAM file
+      pattern: "*.{bai,crai,sai}"
+  - fasta:
+      type: file
+      description: The reference FASTA file
+      pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: file
+      description: The index of the reference FASTA file
+      pattern: "*.fai"
+  - dict:
+      type: file
+      description: The sequence dictionary of the reference FASTA file
+      pattern: "*.dict"
+  - strtablefile:
+      type: file
+      description: The StrTableFile zip folder of the reference FASTA file
+      pattern: "*.zip"
+
+output:
+  #Only when we have meta
+  - 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"
+  - dragstr_model:
+      type: file
+      description: The DragSTR model
+      pattern: "*.txt"
+
+authors:
+  - "@nvnieuwk"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index bf4a6137..d4bfac5b 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -743,6 +743,10 @@ gatk4/calculatecontamination:
   - modules/gatk4/calculatecontamination/**
   - tests/modules/gatk4/calculatecontamination/**
 
+gatk4/calibratedragstrmodel:
+  - modules/gatk4/calibratedragstrmodel/**
+  - tests/modules/gatk4/calibratedragstrmodel/**
+
 gatk4/cnnscorevariants:
   - modules/gatk4/cnnscorevariants/**
   - tests/modules/gatk4/cnnscorevariants/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 39331664..b1326544 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -121,6 +121,7 @@ params {
                 genome_elfasta                                 = "${test_data_dir}/genomics/homo_sapiens/genome/genome.elfasta"
                 genome_fasta                                   = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta"
                 genome_fasta_fai                               = "${test_data_dir}/genomics/homo_sapiens/genome/genome.fasta.fai"
+                genome_strtablefile                            = "${test_data_dir}/genomics/homo_sapiens/genome/genome_strtablefile.zip"
                 genome_dict                                    = "${test_data_dir}/genomics/homo_sapiens/genome/genome.dict"
                 genome_gff3                                    = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
                 genome_gtf                                     = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
diff --git a/tests/modules/gatk4/calibratedragstrmodel/main.nf b/tests/modules/gatk4/calibratedragstrmodel/main.nf
new file mode 100644
index 00000000..4d4e9896
--- /dev/null
+++ b/tests/modules/gatk4/calibratedragstrmodel/main.nf
@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_CALIBRATEDRAGSTRMODEL } from '../../../../modules/gatk4/calibratedragstrmodel/main.nf'
+
+workflow test_gatk4_calibratedragstrmodel_bam {
+    
+    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_bai'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
+
+    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
+}
+
+workflow test_gatk4_calibratedragstrmodel_cram {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+    ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    strtablefile = file(params.test_data['homo_sapiens']['genome']['genome_strtablefile'], checkIfExists: true)
+
+    GATK4_CALIBRATEDRAGSTRMODEL ( input, fasta, fasta_fai, dict, strtablefile )
+}
+
diff --git a/tests/modules/gatk4/calibratedragstrmodel/nextflow.config b/tests/modules/gatk4/calibratedragstrmodel/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/gatk4/calibratedragstrmodel/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/gatk4/calibratedragstrmodel/test.yml b/tests/modules/gatk4/calibratedragstrmodel/test.yml
new file mode 100644
index 00000000..bc46dead
--- /dev/null
+++ b/tests/modules/gatk4/calibratedragstrmodel/test.yml
@@ -0,0 +1,17 @@
+- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam
+  command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_bam -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calibratedragstrmodel
+  files:
+    - path: output/gatk4/test.txt
+      md5sum: 0a1a1583b157fa2251dd931ed165da4f
+
+- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram
+  command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_cram -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/calibratedragstrmodel
+  files:
+    - path: output/gatk4/test.txt
+      md5sum: 1aa7ab38023f724877b3323c5e6b9a4e

From d3874bbae9035e6be95be42a712acfff4d28d00e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 2 Jun 2022 13:22:55 +0200
Subject: [PATCH 19/28] linting

---
 modules/gatk4/calibratedragstrmodel/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gatk4/calibratedragstrmodel/meta.yml b/modules/gatk4/calibratedragstrmodel/meta.yml
index f72a4f60..e6d2b0b1 100644
--- a/modules/gatk4/calibratedragstrmodel/meta.yml
+++ b/modules/gatk4/calibratedragstrmodel/meta.yml
@@ -1,4 +1,4 @@
-name: "gatk4_calibratedragstrmodel"
+name: gatk4_calibratedragstrmodel
 description: estimates the parameters for the DRAGstr model
 keywords:
   - gatk4

From 3a49b82863d6dc71fcfcb36a01b04cb58dcb6f12 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Thu, 2 Jun 2022 13:39:44 +0200
Subject: [PATCH 20/28] Update modules/gatk4/calibratedragstrmodel/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 modules/gatk4/calibratedragstrmodel/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/gatk4/calibratedragstrmodel/main.nf b/modules/gatk4/calibratedragstrmodel/main.nf
index 6682753d..00a11de0 100644
--- a/modules/gatk4/calibratedragstrmodel/main.nf
+++ b/modules/gatk4/calibratedragstrmodel/main.nf
@@ -1,4 +1,4 @@
-process GATK4_CALIBRATEDRAGSTRMODEL{
+process GATK4_CALIBRATEDRAGSTRMODEL {
     tag "$meta.id"
     label 'process_low'
 

From e53d091a6de1ae9fd681351c085d8abe076ba1ec Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 2 Jun 2022 14:08:09 +0200
Subject: [PATCH 21/28] added dragstr model to haplotypecaller

---
 modules/gatk4/haplotypecaller/main.nf        |  4 +++-
 modules/gatk4/haplotypecaller/meta.yml       |  4 ++++
 tests/config/test_data.config                |  2 ++
 tests/modules/gatk4/haplotypecaller/main.nf  | 22 +++++++++++++++++++-
 tests/modules/gatk4/haplotypecaller/test.yml | 18 ++++++++++------
 5 files changed, 42 insertions(+), 8 deletions(-)

diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf
index 6dd3f69e..19cd57bb 100644
--- a/modules/gatk4/haplotypecaller/main.nf
+++ b/modules/gatk4/haplotypecaller/main.nf
@@ -8,7 +8,7 @@ process GATK4_HAPLOTYPECALLER {
         'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(input), path(input_index), path(intervals)
+    tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
     path  fasta
     path  fai
     path  dict
@@ -28,6 +28,7 @@ process GATK4_HAPLOTYPECALLER {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
     def interval_command = intervals ? "--intervals $intervals" : ""
+    def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : ""
 
     def avail_mem = 3
     if (!task.memory) {
@@ -42,6 +43,7 @@ process GATK4_HAPLOTYPECALLER {
         --reference $fasta \\
         $dbsnp_command \\
         $interval_command \\
+        $dragstr_command \\
         --tmp-dir . \\
         $args
 
diff --git a/modules/gatk4/haplotypecaller/meta.yml b/modules/gatk4/haplotypecaller/meta.yml
index 81851a96..48193d91 100644
--- a/modules/gatk4/haplotypecaller/meta.yml
+++ b/modules/gatk4/haplotypecaller/meta.yml
@@ -32,6 +32,10 @@ input:
   - intervals:
       type: file
       description: Bed file with the genomic regions included in the library (optional)
+  - dragstr_model:
+      type: file
+      description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
+      pattern: "*.txt"
   - fasta:
       type: file
       description: The reference fasta file
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 363903f0..fa7017b1 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -266,6 +266,8 @@ params {
                 test_pileups_table                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
                 test2_pileups_table                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
 
+                test_paired_end_sorted_dragstrmodel            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt"
+
                 test_genomicsdb_tar_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
                 test_pon_genomicsdb_tar_gz                     = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
 
diff --git a/tests/modules/gatk4/haplotypecaller/main.nf b/tests/modules/gatk4/haplotypecaller/main.nf
index 7b60baab..3ad3dfb5 100644
--- a/tests/modules/gatk4/haplotypecaller/main.nf
+++ b/tests/modules/gatk4/haplotypecaller/main.nf
@@ -8,6 +8,7 @@ workflow test_gatk4_haplotypecaller {
     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),
+                  [],
                   []
                 ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
@@ -21,6 +22,7 @@ workflow test_gatk4_haplotypecaller_cram {
     input = [ [ id:'test' ], // meta map
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                [],
                 []
               ]
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@@ -34,7 +36,8 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
    input = [ [ id:'test' ], // meta map
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
                 file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
-                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
+                []
             ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@@ -45,3 +48,20 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
 
     GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
 }
+
+workflow test_gatk4_haplotypecaller_dragstr_model {
+   input = [ [ id:'test' ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                [],
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], 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)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+    sites = []
+    sites_tbi = []
+
+    GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
+}
diff --git a/tests/modules/gatk4/haplotypecaller/test.yml b/tests/modules/gatk4/haplotypecaller/test.yml
index 3d416a0d..b566ee66 100644
--- a/tests/modules/gatk4/haplotypecaller/test.yml
+++ b/tests/modules/gatk4/haplotypecaller/test.yml
@@ -1,29 +1,35 @@
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
   tags:
     - gatk4/haplotypecaller
     - gatk4
   files:
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
 
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
   tags:
     - gatk4/haplotypecaller
     - gatk4
   files:
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml
 
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  tags:
+    - gatk4/haplotypecaller
+    - gatk4
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.tbi
+
+- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
   tags:
     - gatk4/haplotypecaller
     - gatk4
   files:
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
-    - path: output/gatk4/versions.yml

From a6c4276ad74eb965fd9d8eb831f0786b85abc9c8 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Thu, 2 Jun 2022 14:19:57 +0200
Subject: [PATCH 22/28] Update tests/modules/gatk4/haplotypecaller/test.yml

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

diff --git a/tests/modules/gatk4/haplotypecaller/test.yml b/tests/modules/gatk4/haplotypecaller/test.yml
index b566ee66..ca3110d7 100644
--- a/tests/modules/gatk4/haplotypecaller/test.yml
+++ b/tests/modules/gatk4/haplotypecaller/test.yml
@@ -1,5 +1,5 @@
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
   tags:
     - gatk4/haplotypecaller
     - gatk4

From 2ce1cf3329eecc636ddfcbf27f86b398b45ac0ad Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Thu, 2 Jun 2022 14:20:04 +0200
Subject: [PATCH 23/28] Update tests/modules/gatk4/haplotypecaller/test.yml

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

diff --git a/tests/modules/gatk4/haplotypecaller/test.yml b/tests/modules/gatk4/haplotypecaller/test.yml
index ca3110d7..094beaef 100644
--- a/tests/modules/gatk4/haplotypecaller/test.yml
+++ b/tests/modules/gatk4/haplotypecaller/test.yml
@@ -8,7 +8,7 @@
     - path: output/gatk4/test.vcf.gz.tbi
 
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
   tags:
     - gatk4/haplotypecaller
     - gatk4

From e419d306dfeb8bab0e1d3ac07151585c0fcbee01 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Thu, 2 Jun 2022 14:20:10 +0200
Subject: [PATCH 24/28] Update tests/modules/gatk4/haplotypecaller/test.yml

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

diff --git a/tests/modules/gatk4/haplotypecaller/test.yml b/tests/modules/gatk4/haplotypecaller/test.yml
index 094beaef..17c4f6bf 100644
--- a/tests/modules/gatk4/haplotypecaller/test.yml
+++ b/tests/modules/gatk4/haplotypecaller/test.yml
@@ -17,7 +17,7 @@
     - path: output/gatk4/test.vcf.gz.tbi
 
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
   tags:
     - gatk4/haplotypecaller
     - gatk4

From e107d61069612fca5aaabcd4f056d06c732d0c18 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Thu, 2 Jun 2022 14:20:15 +0200
Subject: [PATCH 25/28] Update tests/modules/gatk4/haplotypecaller/test.yml

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

diff --git a/tests/modules/gatk4/haplotypecaller/test.yml b/tests/modules/gatk4/haplotypecaller/test.yml
index 17c4f6bf..96270644 100644
--- a/tests/modules/gatk4/haplotypecaller/test.yml
+++ b/tests/modules/gatk4/haplotypecaller/test.yml
@@ -26,7 +26,7 @@
     - path: output/gatk4/test.vcf.gz.tbi
 
 - name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
-  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
+  command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
   tags:
     - gatk4/haplotypecaller
     - gatk4

From 046fa3958223ce4542578ef26502d39f4c5d71ef Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 2 Jun 2022 16:09:09 +0200
Subject: [PATCH 26/28] update VEP version + cache

---
 modules/ensemblvep/Dockerfile      |  4 ++--
 modules/ensemblvep/build.sh        | 12 ++++++------
 modules/ensemblvep/environment.yml |  4 ++--
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/ensemblvep/Dockerfile b/modules/ensemblvep/Dockerfile
index b4a1c664..4ada7c6b 100644
--- a/modules/ensemblvep/Dockerfile
+++ b/modules/ensemblvep/Dockerfile
@@ -11,8 +11,8 @@ RUN conda env create -f /environment.yml && conda clean -a
 # Setup default ARG variables
 ARG GENOME=GRCh38
 ARG SPECIES=homo_sapiens
-ARG VEP_VERSION=104
-ARG VEP_TAG=104.3
+ARG VEP_VERSION=105
+ARG VEP_TAG=105.0
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
 ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH
diff --git a/modules/ensemblvep/build.sh b/modules/ensemblvep/build.sh
index 650c8704..402f2434 100755
--- a/modules/ensemblvep/build.sh
+++ b/modules/ensemblvep/build.sh
@@ -20,9 +20,9 @@ build_push() {
     docker push nfcore/vep:${VEP_TAG}.${GENOME}
 }
 
-build_push "GRCh37"    "homo_sapiens"           "104" "104.3"
-build_push "GRCh38"    "homo_sapiens"           "104" "104.3"
-build_push "GRCm38"    "mus_musculus"           "102" "104.3"
-build_push "GRCm39"    "mus_musculus"           "104" "104.3"
-build_push "CanFam3.1" "canis_lupus_familiaris" "104" "104.3"
-build_push "WBcel235"  "caenorhabditis_elegans" "104" "104.3"
+build_push "GRCh37"    "homo_sapiens"           "105" "105.0"
+build_push "GRCh38"    "homo_sapiens"           "105" "105.0"
+build_push "GRCm38"    "mus_musculus"           "102" "105.0"
+build_push "GRCm39"    "mus_musculus"           "105" "105.0"
+build_push "CanFam3.1" "canis_lupus_familiaris" "105" "105.0"
+build_push "WBcel235"  "caenorhabditis_elegans" "105" "105.0"
diff --git a/modules/ensemblvep/environment.yml b/modules/ensemblvep/environment.yml
index c0731c26..5df85b80 100644
--- a/modules/ensemblvep/environment.yml
+++ b/modules/ensemblvep/environment.yml
@@ -1,10 +1,10 @@
 # You can use this file to create a conda environment for this module:
 #   conda env create -f environment.yml
-name: nf-core-vep-104.3
+name: nf-core-vep-105.0
 channels:
   - conda-forge
   - bioconda
   - defaults
 
 dependencies:
-  - bioconda::ensembl-vep=104.3
+  - bioconda::ensembl-vep=105.0

From bc0f52bcd3a64f27d8fb2da3a6424b427e15e53c Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 2 Jun 2022 16:11:11 +0200
Subject: [PATCH 27/28] fix cache version

---
 modules/ensemblvep/build.sh | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/ensemblvep/build.sh b/modules/ensemblvep/build.sh
index 402f2434..e21a7c0d 100755
--- a/modules/ensemblvep/build.sh
+++ b/modules/ensemblvep/build.sh
@@ -20,9 +20,9 @@ build_push() {
     docker push nfcore/vep:${VEP_TAG}.${GENOME}
 }
 
-build_push "GRCh37"    "homo_sapiens"           "105" "105.0"
-build_push "GRCh38"    "homo_sapiens"           "105" "105.0"
-build_push "GRCm38"    "mus_musculus"           "102" "105.0"
-build_push "GRCm39"    "mus_musculus"           "105" "105.0"
-build_push "CanFam3.1" "canis_lupus_familiaris" "105" "105.0"
-build_push "WBcel235"  "caenorhabditis_elegans" "105" "105.0"
+# build_push "GRCh37"    "homo_sapiens"           "105" "105.0"
+# build_push "GRCh38"    "homo_sapiens"           "105" "105.0"
+# build_push "GRCm38"    "mus_musculus"           "102" "105.0"
+# build_push "GRCm39"    "mus_musculus"           "105" "105.0"
+build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0"
+# build_push "WBcel235"  "caenorhabditis_elegans" "105" "105.0"

From b623ff5d2798b8c955baeb3890f0baee6077db66 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 2 Jun 2022 16:11:45 +0200
Subject: [PATCH 28/28] fix comments

---
 modules/ensemblvep/build.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/ensemblvep/build.sh b/modules/ensemblvep/build.sh
index e21a7c0d..6f340c0f 100755
--- a/modules/ensemblvep/build.sh
+++ b/modules/ensemblvep/build.sh
@@ -20,9 +20,9 @@ build_push() {
     docker push nfcore/vep:${VEP_TAG}.${GENOME}
 }
 
-# build_push "GRCh37"    "homo_sapiens"           "105" "105.0"
-# build_push "GRCh38"    "homo_sapiens"           "105" "105.0"
-# build_push "GRCm38"    "mus_musculus"           "102" "105.0"
-# build_push "GRCm39"    "mus_musculus"           "105" "105.0"
+build_push "GRCh37"    "homo_sapiens"           "105" "105.0"
+build_push "GRCh38"    "homo_sapiens"           "105" "105.0"
+build_push "GRCm38"    "mus_musculus"           "102" "105.0"
+build_push "GRCm39"    "mus_musculus"           "105" "105.0"
 build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0"
-# build_push "WBcel235"  "caenorhabditis_elegans" "105" "105.0"
+build_push "WBcel235"  "caenorhabditis_elegans" "105" "105.0"