From 024c992ca77d6bf5e4baddae30a38cd14d526042 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 27 Apr 2022 11:12:58 +0200
Subject: [PATCH 01/37] created the module

---
 modules/vardictjava/main.nf               | 77 +++++++++++++++++++++++
 modules/vardictjava/meta.yml              | 51 +++++++++++++++
 tests/config/pytest_modules.yml           |  4 ++
 tests/modules/vardictjava/main.nf         | 15 +++++
 tests/modules/vardictjava/nextflow.config |  8 +++
 tests/modules/vardictjava/test.yml        | 12 ++++
 6 files changed, 167 insertions(+)
 create mode 100644 modules/vardictjava/main.nf
 create mode 100644 modules/vardictjava/meta.yml
 create mode 100644 tests/modules/vardictjava/main.nf
 create mode 100644 tests/modules/vardictjava/nextflow.config
 create mode 100644 tests/modules/vardictjava/test.yml

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
new file mode 100644
index 00000000..d52e15dd
--- /dev/null
+++ b/modules/vardictjava/main.nf
@@ -0,0 +1,77 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process VARDICTJAVA {
+    tag "$meta.id"
+    label 'process_medium'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
+        'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    tuple val(meta), path(bam)
+    path(reference_fasta)
+    path(regions_of_interest)
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*.bam"), emit: bam
+    // TODO nf-core: List additional required output channels/values here
+    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}"
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    """
+    vardict-java \\
+        $args \\
+        -b $bam \\
+        -th $task.cpus \\
+        -n $prefix \\
+        -G $reference_fasta \\
+        $regions_of_interest \\
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vardictjava: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
new file mode 100644
index 00000000..e8c55de3
--- /dev/null
+++ b/modules/vardictjava/meta.yml
@@ -0,0 +1,51 @@
+name: "vardictjava"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "vardictjava":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Java port of the VarDict variant discovery program"
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      doi: ""
+      licence: "['MIT']"
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  # 
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+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"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@nvnieuwk"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4d8ce0b5..8ca9f2e2 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1908,6 +1908,10 @@ unzip:
   - modules/unzip/**
   - tests/modules/unzip/**
 
+vardictjava:
+  - modules/vardictjava/**
+  - tests/modules/vardictjava/**
+
 variantbam:
   - modules/variantbam/**
   - tests/modules/variantbam/**
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
new file mode 100644
index 00000000..8a714b2b
--- /dev/null
+++ b/tests/modules/vardictjava/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
+
+workflow test_vardictjava {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    VARDICTJAVA ( input )
+}
diff --git a/tests/modules/vardictjava/nextflow.config b/tests/modules/vardictjava/nextflow.config
new file mode 100644
index 00000000..5dc176a9
--- /dev/null
+++ b/tests/modules/vardictjava/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+    withName: VARDICTJAVA {
+        ext.args = ''
+    }
+}
\ No newline at end of file
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
new file mode 100644
index 00000000..73c647af
--- /dev/null
+++ b/tests/modules/vardictjava/test.yml
@@ -0,0 +1,12 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml vardictjava
+- name: "vardictjava"
+  command: nextflow run ./tests/modules/vardictjava -entry test_vardictjava -c ./tests/config/nextflow.config -c ./tests/modules/vardictjava/nextflow.config
+  tags:
+    - "vardictjava"
+    #
+  files:
+    - path: "output/vardictjava/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/vardictjava/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b

From d57664b576d2433deed1b0fb742f3a3da05d5046 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Wed, 27 Apr 2022 11:18:58 +0200
Subject: [PATCH 02/37] cleanup TODO's

---
 modules/vardictjava/main.nf | 39 +------------------------------------
 1 file changed, 1 insertion(+), 38 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index d52e15dd..80beb540 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -1,48 +1,19 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process VARDICTJAVA {
     tag "$meta.id"
     label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
         'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
     tuple val(meta), path(bam)
     path(reference_fasta)
     path(regions_of_interest)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
     path "versions.yml"           , emit: versions
 
     when:
@@ -51,15 +22,7 @@ process VARDICTJAVA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+
     """
     vardict-java \\
         $args \\

From 7956d38e61a8efdd2fffcb6cf33f4a02ad73bc50 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 27 Apr 2022 13:18:46 +0200
Subject: [PATCH 03/37] Fixed the test on nextflow level

---
 modules/vardictjava/main.nf        |  4 +--
 modules/vardictjava/meta.yml       | 46 ++++++++++++++++++------------
 tests/modules/vardictjava/main.nf  |  8 ++++--
 tests/modules/vardictjava/test.yml |  2 +-
 4 files changed, 36 insertions(+), 24 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 80beb540..8170bf76 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -13,7 +13,7 @@ process VARDICTJAVA {
     path(regions_of_interest)
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.vcf"), emit: vcf
     path "versions.yml"           , emit: versions
 
     when:
@@ -34,7 +34,7 @@ process VARDICTJAVA {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vardictjava: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        vardictjava: \$(echo 1.8.3)
     END_VERSIONS
     """
 }
diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index e8c55de3..7820a877 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -1,19 +1,19 @@
 name: "vardictjava"
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+
+description: The Java port of the VarDict variant caller
 keywords:
-  - sort
+  - variant calling
+  - VarDict
+  - AstraZeneca
 tools:
   - "vardictjava":
-      ## TODO nf-core: Add a description and other details for the software below
       description: "Java port of the VarDict variant discovery program"
-      homepage: "None"
-      documentation: "None"
-      tool_dev_url: "None"
-      doi: ""
+      homepage: "https://github.com/AstraZeneca-NGS/VarDictJava"
+      documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
+      tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
+      doi: "10.1093/nar/gkw227 "
       licence: "['MIT']"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   # Only when we have meta
   - meta:
@@ -21,14 +21,22 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
-  ## TODO nf-core: Delete / customise this example input
+
   - bam:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: BAM/SAM file
+      pattern: "*.{bam,sam}"
+  
+  - reference_fasta:
+      type: file
+      description: FASTA of the reference genome
+      pattern: "*.{fa,fasta}"
+
+  - regions_of_interest:
+      type: file
+      description: BED with the regions of interest
+      pattern: "*.bed"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
   #Only when we have meta
   - meta:
@@ -36,16 +44,16 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
+
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
+
+  - vcf:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: VCF file output
+      pattern: "*.vcf"
 
 authors:
   - "@nvnieuwk"
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
index 8a714b2b..7511b529 100644
--- a/tests/modules/vardictjava/main.nf
+++ b/tests/modules/vardictjava/main.nf
@@ -8,8 +8,12 @@ workflow test_vardictjava {
     
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
 
-    VARDICTJAVA ( input )
+    VARDICTJAVA ( 
+        input, 
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) 
+    )
 }
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 73c647af..001a56e8 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -6,7 +6,7 @@
     - "vardictjava"
     #
   files:
-    - path: "output/vardictjava/test.bam"
+    - path: "output/vardictjava/test.vcf"
       md5sum: e667c7caad0bc4b7ac383fd023c654fc
     - path: output/vardictjava/versions.yml
       md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b

From 85c49a971f91208ead572212be8475f5e7518feb Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 09:07:52 +0200
Subject: [PATCH 04/37] Fixed an issue with wrong file order

---
 modules/vardictjava/main.nf | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 8170bf76..855784db 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -8,9 +8,8 @@ process VARDICTJAVA {
         'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(regions_of_interest)
     path(reference_fasta)
-    path(regions_of_interest)
 
     output:
     tuple val(meta), path("*.vcf"), emit: vcf
@@ -24,6 +23,9 @@ process VARDICTJAVA {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
+    head -n 20 $reference_fasta
+    cat $reference_fasta | wc -l
+
     vardict-java \\
         $args \\
         -b $bam \\
@@ -31,10 +33,11 @@ process VARDICTJAVA {
         -n $prefix \\
         -G $reference_fasta \\
         $regions_of_interest \\
+        > ${prefix}.vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vardictjava: \$(echo 1.8.3)
+        vardict-java: \$(echo 1.8.3)
     END_VERSIONS
     """
 }

From db43095b1a1530af1e3cac7f3e7211c52d87bbd7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 09:18:15 +0200
Subject: [PATCH 05/37] Split the bed file into a seperate input

---
 modules/vardictjava/main.nf       |  8 +++-----
 tests/modules/vardictjava/main.nf | 14 +++++++-------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 855784db..e1098b22 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -8,7 +8,8 @@ process VARDICTJAVA {
         'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(regions_of_interest)
+    tuple val(meta), path(bam) 
+    path(regions_of_interest)
     path(reference_fasta)
 
     output:
@@ -23,14 +24,11 @@ process VARDICTJAVA {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    head -n 20 $reference_fasta
-    cat $reference_fasta | wc -l
-
     vardict-java \\
         $args \\
         -b $bam \\
         -th $task.cpus \\
-        -n $prefix \\
+        -N $prefix \\
         -G $reference_fasta \\
         $regions_of_interest \\
         > ${prefix}.vcf
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
index 7511b529..647c8bba 100644
--- a/tests/modules/vardictjava/main.nf
+++ b/tests/modules/vardictjava/main.nf
@@ -6,14 +6,14 @@ include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
 
 workflow test_vardictjava {
     
-    input = [
+    bam_input_ch = Channel.of([
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
-    ]
+    ])
 
-    VARDICTJAVA ( 
-        input, 
-        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) 
-    )
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    VARDICTJAVA ( bam_input_ch, bed, fasta )
 }

From def580ddb7af11619f8f0757ef5af5ed156ed6a4 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 09:28:57 +0200
Subject: [PATCH 06/37] Add gzip for compressed output

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

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index e1098b22..425c1706 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -31,7 +31,7 @@ process VARDICTJAVA {
         -N $prefix \\
         -G $reference_fasta \\
         $regions_of_interest \\
-        > ${prefix}.vcf
+        | gzip -c > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 484c8f5dfa40a2117997afcd8434bcd52ff4fe4e Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 09:29:27 +0200
Subject: [PATCH 07/37] Update meta.yml

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

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 7820a877..5bc21b55 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -53,7 +53,7 @@ output:
   - vcf:
       type: file
       description: VCF file output
-      pattern: "*.vcf"
+      pattern: "*.vcf.gz"
 
 authors:
   - "@nvnieuwk"

From 9df830f79dc70a347578120e797a4e3160dfc66d Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 10:23:07 +0200
Subject: [PATCH 08/37] Added the .bai and .fai files

---
 modules/vardictjava/main.nf        |  8 ++++----
 tests/modules/vardictjava/main.nf  | 12 ++++++++----
 tests/modules/vardictjava/test.yml | 15 ++++++---------
 3 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 425c1706..c370b6ef 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -8,12 +8,12 @@ process VARDICTJAVA {
         'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam) 
+    tuple val(meta), path(bam), path(bai)
     path(regions_of_interest)
-    path(reference_fasta)
+    tuple path(reference_fasta), path(reference_fai)
 
     output:
-    tuple val(meta), path("*.vcf"), emit: vcf
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
     path "versions.yml"           , emit: versions
 
     when:
@@ -30,7 +30,7 @@ process VARDICTJAVA {
         -th $task.cpus \\
         -N $prefix \\
         -G $reference_fasta \\
-        $regions_of_interest \\
+        $regions_of_interest
         | gzip -c > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
index 647c8bba..89eec407 100644
--- a/tests/modules/vardictjava/main.nf
+++ b/tests/modules/vardictjava/main.nf
@@ -8,12 +8,16 @@ workflow test_vardictjava {
     
     bam_input_ch = Channel.of([
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
     ])
 
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
 
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    reference = Channel.of([
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    ])
 
-    VARDICTJAVA ( bam_input_ch, bed, fasta )
+    VARDICTJAVA ( bam_input_ch, bed, reference )
 }
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 001a56e8..77aa9047 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -1,12 +1,9 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml vardictjava
-- name: "vardictjava"
-  command: nextflow run ./tests/modules/vardictjava -entry test_vardictjava -c ./tests/config/nextflow.config -c ./tests/modules/vardictjava/nextflow.config
+- name: vardictjava test_vardictjava
+  command: nextflow run tests/modules/vardictjava -entry test_vardictjava -c tests/config/nextflow.config
   tags:
-    - "vardictjava"
-    #
+    - vardictjava
   files:
-    - path: "output/vardictjava/test.vcf"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/vardictjava/test.vcf.gz
+      md5sum: 2179dcaee6183495b421293f42db11b5
     - path: output/vardictjava/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+      md5sum: aac455b8c9c9194c5fed80e4fd495b96

From 45b4a61a15c8b7ac6c29a447ccc1ece9f08f8efe Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 13:31:37 +0200
Subject: [PATCH 09/37] Some small updates

---
 modules/vardictjava/main.nf        | 2 +-
 tests/modules/vardictjava/main.nf  | 8 ++++----
 tests/modules/vardictjava/test.yml | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index c370b6ef..26833436 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -30,7 +30,7 @@ process VARDICTJAVA {
         -th $task.cpus \\
         -N $prefix \\
         -G $reference_fasta \\
-        $regions_of_interest
+        $regions_of_interest \\
         | gzip -c > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf
index 89eec407..d392358a 100644
--- a/tests/modules/vardictjava/main.nf
+++ b/tests/modules/vardictjava/main.nf
@@ -6,15 +6,15 @@ include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'
 
 workflow test_vardictjava {
     
-    bam_input_ch = Channel.of([
-        [ id:'test', single_end:false ], // meta map
+    bam_input_ch = Channel.value([
+        [ id:'test' ], // 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)
     ])
 
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
+    bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true))
 
-    reference = Channel.of([
+    reference = Channel.value([
         file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     ])
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 77aa9047..0bd21f4e 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -4,6 +4,6 @@
     - vardictjava
   files:
     - path: output/vardictjava/test.vcf.gz
-      md5sum: 2179dcaee6183495b421293f42db11b5
+      md5sum: 7029066c27ac6f5ef18d660d5741979a
     - path: output/vardictjava/versions.yml
       md5sum: aac455b8c9c9194c5fed80e4fd495b96

From 8c98a78d2a0e12d081184736e17ccde3feee3f44 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 14:07:55 +0200
Subject: [PATCH 10/37] Fixed the issue with the BED file

---
 modules/vardictjava/main.nf        | 1 +
 tests/modules/vardictjava/test.yml | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 26833436..d6b4f1dd 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -26,6 +26,7 @@ process VARDICTJAVA {
     """
     vardict-java \\
         $args \\
+        -c 1 -S 2 -E 3 \\
         -b $bam \\
         -th $task.cpus \\
         -N $prefix \\
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 0bd21f4e..77aa9047 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -4,6 +4,6 @@
     - vardictjava
   files:
     - path: output/vardictjava/test.vcf.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      md5sum: 2179dcaee6183495b421293f42db11b5
     - path: output/vardictjava/versions.yml
       md5sum: aac455b8c9c9194c5fed80e4fd495b96

From bf186044716cb0621f31ccc4727ad4a0fb7c81b9 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 14:29:37 +0200
Subject: [PATCH 11/37] fix for a linting issue

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

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index d6b4f1dd..3e036ebd 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -14,7 +14,7 @@ process VARDICTJAVA {
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "versions.yml"           , emit: versions
+    path "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From 40e6e5273de785042fc1b4d6fc1d7510729a7789 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 14:30:04 +0200
Subject: [PATCH 12/37] fix for a linting issue

---
 modules/vardictjava/meta.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 5bc21b55..39368f81 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -15,7 +15,6 @@ tools:
       licence: "['MIT']"
 
 input:
-  # Only when we have meta
   - meta:
       type: map
       description: |
@@ -38,7 +37,6 @@ input:
       pattern: "*.bed"
 
 output:
-  #Only when we have meta
   - meta:
       type: map
       description: |

From 6678ad4426664076d912dab488ea641f44c1fdb6 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 14:54:20 +0200
Subject: [PATCH 13/37] Added a header to the VCF

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

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 3e036ebd..a28cb539 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -26,7 +26,7 @@ process VARDICTJAVA {
     """
     vardict-java \\
         $args \\
-        -c 1 -S 2 -E 3 \\
+        -c 1 -S 2 -E 3 -h \\
         -b $bam \\
         -th $task.cpus \\
         -N $prefix \\

From bdff37c3d7c880f599af223504808306e75e2d76 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 15:33:27 +0200
Subject: [PATCH 14/37] Added the statistical tests and conversion to vcf

---
 modules/vardictjava/main.nf               | 7 ++++++-
 tests/modules/vardictjava/nextflow.config | 1 +
 tests/modules/vardictjava/test.yml        | 2 +-
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index a28cb539..92051074 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -21,17 +21,22 @@ process VARDICTJAVA {
 
     script:
     def args = task.ext.args ?: ''
+    def args_conversion = task.ext.args_conversion ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     vardict-java \\
         $args \\
-        -c 1 -S 2 -E 3 -h \\
+        -c 1 -S 2 -E 3 \\
         -b $bam \\
         -th $task.cpus \\
         -N $prefix \\
         -G $reference_fasta \\
         $regions_of_interest \\
+        | teststrandbias.R \\
+        | var2vcf_valid.pl \\
+            $args_conversion \\
+            -N $prefix \\
         | gzip -c > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/vardictjava/nextflow.config b/tests/modules/vardictjava/nextflow.config
index 5dc176a9..fc698f59 100644
--- a/tests/modules/vardictjava/nextflow.config
+++ b/tests/modules/vardictjava/nextflow.config
@@ -4,5 +4,6 @@ process {
     
     withName: VARDICTJAVA {
         ext.args = ''
+        ext.args_conversion = ''
     }
 }
\ No newline at end of file
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 77aa9047..549d688e 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -4,6 +4,6 @@
     - vardictjava
   files:
     - path: output/vardictjava/test.vcf.gz
-      md5sum: 2179dcaee6183495b421293f42db11b5
+      md5sum: 3f1f227afc532bddeb58f16fd3013fc8
     - path: output/vardictjava/versions.yml
       md5sum: aac455b8c9c9194c5fed80e4fd495b96

From d626a1dcd3ca759c2c398efe49642a39d843ecd7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 15:41:43 +0200
Subject: [PATCH 15/37] Removed a whitespace in meta.yml...

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

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 39368f81..e3b2efe7 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -25,7 +25,7 @@ input:
       type: file
       description: BAM/SAM file
       pattern: "*.{bam,sam}"
-  
+
   - reference_fasta:
       type: file
       description: FASTA of the reference genome

From 4b04ca22ddc577951bc59a693e247c6ff5949dd7 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 28 Apr 2022 16:38:49 +0200
Subject: [PATCH 16/37] Variable name change for var2vcf conversion arguments

---
 modules/vardictjava/main.nf               | 4 ++--
 tests/modules/vardictjava/nextflow.config | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 92051074..08318c29 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -21,7 +21,7 @@ process VARDICTJAVA {
 
     script:
     def args = task.ext.args ?: ''
-    def args_conversion = task.ext.args_conversion ?: ''
+    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
@@ -35,7 +35,7 @@ process VARDICTJAVA {
         $regions_of_interest \\
         | teststrandbias.R \\
         | var2vcf_valid.pl \\
-            $args_conversion \\
+            $args2 \\
             -N $prefix \\
         | gzip -c > ${prefix}.vcf.gz
 
diff --git a/tests/modules/vardictjava/nextflow.config b/tests/modules/vardictjava/nextflow.config
index fc698f59..e08201cc 100644
--- a/tests/modules/vardictjava/nextflow.config
+++ b/tests/modules/vardictjava/nextflow.config
@@ -4,6 +4,6 @@ process {
     
     withName: VARDICTJAVA {
         ext.args = ''
-        ext.args_conversion = ''
+        ext.args2 = ''
     }
 }
\ No newline at end of file

From 6b64f9cb6c3dd3577931cc3cd032d6fb730000ce Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 10:34:14 +0200
Subject: [PATCH 17/37] feat added stub to modules

---
 modules/gatk4/mergebamalignment/main.nf | 11 +++++++++++
 modules/gatk4/mutect2/main.nf           | 14 ++++++++++++++
 modules/gatk4/revertsam/main.nf         | 11 +++++++++++
 modules/gatk4/samtofastq/main.nf        | 13 +++++++++++++
 modules/samtools/view/main.nf           | 12 ++++++++++++
 5 files changed, 61 insertions(+)

diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf
index 7ba9ccda..5c36b4ba 100644
--- a/modules/gatk4/mergebamalignment/main.nf
+++ b/modules/gatk4/mergebamalignment/main.nf
@@ -43,4 +43,15 @@ process GATK4_MERGEBAMALIGNMENT {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf
index 4a1f5768..a214b57d 100644
--- a/modules/gatk4/mutect2/main.nf
+++ b/modules/gatk4/mutect2/main.nf
@@ -57,4 +57,18 @@ process GATK4_MUTECT2 {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.tbi
+    touch ${prefix}.stats
+    touch ${prefix}.f1r2.tar.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf
index 4e8e9ddc..3084658d 100644
--- a/modules/gatk4/revertsam/main.nf
+++ b/modules/gatk4/revertsam/main.nf
@@ -39,4 +39,15 @@ process GATK4_REVERTSAM {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.reverted.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf
index 8553e419..d8d94d69 100644
--- a/modules/gatk4/samtofastq/main.nf
+++ b/modules/gatk4/samtofastq/main.nf
@@ -40,4 +40,17 @@ process GATK4_SAMTOFASTQ {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fastq.gz
+    touch ${prefix}_1.fastq.gz
+    touch ${prefix}_2.fastq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf
index 11cfb74b..55194e88 100644
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@@ -41,4 +41,16 @@ process SAMTOOLS_VIEW {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }

From 8a5bcbc325d20f081c9a722bc47f380df43448b7 Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 11:06:08 +0200
Subject: [PATCH 18/37] fix the stub of gatk4_revertsam

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

diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf
index 3084658d..162aa0fa 100644
--- a/modules/gatk4/revertsam/main.nf
+++ b/modules/gatk4/revertsam/main.nf
@@ -43,7 +43,7 @@ process GATK4_REVERTSAM {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.reverted.bam
+    touch ${prefix}.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 08d5acbeb6c9e1b113ef3a0f4d32a6a1dbe522fe Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 11:59:08 +0200
Subject: [PATCH 19/37] feat added tests for stubs

---
 tests/modules/gatk4/mergebamalignment/main.nf  | 11 +++++++++++
 tests/modules/gatk4/mergebamalignment/test.yml |  9 +++++++++
 tests/modules/gatk4/mutect2/main.nf            | 18 ++++++++++++++++++
 tests/modules/gatk4/mutect2/test.yml           | 11 +++++++++++
 tests/modules/gatk4/revertsam/main.nf          |  8 ++++++++
 tests/modules/gatk4/revertsam/test.yml         |  9 +++++++++
 tests/modules/gatk4/samtofastq/main.nf         |  8 ++++++++
 tests/modules/gatk4/samtofastq/test.yml        | 10 ++++++++++
 tests/modules/samtools/view/main.nf            |  9 +++++++++
 tests/modules/samtools/view/test.yml           |  8 ++++++++
 10 files changed, 101 insertions(+)

diff --git a/tests/modules/gatk4/mergebamalignment/main.nf b/tests/modules/gatk4/mergebamalignment/main.nf
index 8a38c129..ebedad9b 100644
--- a/tests/modules/gatk4/mergebamalignment/main.nf
+++ b/tests/modules/gatk4/mergebamalignment/main.nf
@@ -14,3 +14,14 @@ workflow test_gatk4_mergebamalignment {
 
     GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
 }
+
+workflow test_gatk4_mergebamalignment_stubs {
+    input    = [ [ id:'test' ], // meta map
+                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
+               ]
+    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
+}
diff --git a/tests/modules/gatk4/mergebamalignment/test.yml b/tests/modules/gatk4/mergebamalignment/test.yml
index b1bb32b2..84a67654 100644
--- a/tests/modules/gatk4/mergebamalignment/test.yml
+++ b/tests/modules/gatk4/mergebamalignment/test.yml
@@ -7,3 +7,12 @@
     - path: output/gatk4/test.bam
       md5sum: e6f1b343700b7ccb94e81ae127433988
     - path: output/gatk4/versions.yml
+
+- name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
+  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/mergebamalignment
+  files:
+    - path: output/gatk4/test.bam
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
index 0b4339f0..619d28b8 100644
--- a/tests/modules/gatk4/mutect2/main.nf
+++ b/tests/modules/gatk4/mutect2/main.nf
@@ -118,3 +118,21 @@ workflow test_gatk4_mutect2_mitochondria {
 
     GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
 }
+
+workflow test_gatk4_mutect2_tumor_single_stubs {
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
+              []
+            ]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+
+    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+}
diff --git a/tests/modules/gatk4/mutect2/test.yml b/tests/modules/gatk4/mutect2/test.yml
index 3cefce09..9232cedd 100644
--- a/tests/modules/gatk4/mutect2/test.yml
+++ b/tests/modules/gatk4/mutect2/test.yml
@@ -69,3 +69,14 @@
       md5sum: fc6ea14ca2da346babe78161beea28c9
     - path: output/gatk4/test.vcf.gz.tbi
     - path: output/gatk4/versions.yml
+
+- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single_stubs
+  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/mutect2
+  files:
+    - path: output/gatk4/test.vcf.gz
+    - path: output/gatk4/test.vcf.gz.stats
+    - path: output/gatk4/test.vcf.gz.tbi
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/revertsam/main.nf b/tests/modules/gatk4/revertsam/main.nf
index ab5dddee..5b14d471 100644
--- a/tests/modules/gatk4/revertsam/main.nf
+++ b/tests/modules/gatk4/revertsam/main.nf
@@ -11,3 +11,11 @@ workflow test_gatk4_revertsam {
 
     GATK4_REVERTSAM ( input )
 }
+
+workflow test_gatk4_revertsam_stubs {
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+            ]
+
+    GATK4_REVERTSAM ( input )
+}
diff --git a/tests/modules/gatk4/revertsam/test.yml b/tests/modules/gatk4/revertsam/test.yml
index 2ebdb685..89e78659 100644
--- a/tests/modules/gatk4/revertsam/test.yml
+++ b/tests/modules/gatk4/revertsam/test.yml
@@ -7,3 +7,12 @@
     - path: output/gatk4/test.reverted.bam
       md5sum: f783a88deb45c3a2c20ca12cbe1c5652
     - path: output/gatk4/versions.yml
+
+- name: gatk4 revertsam test_gatk4_revertsam_stubs
+  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/revertsam
+  files:
+    - path: output/gatk4/test.reverted.bam
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/gatk4/samtofastq/main.nf b/tests/modules/gatk4/samtofastq/main.nf
index 26a8ce2d..aad80057 100644
--- a/tests/modules/gatk4/samtofastq/main.nf
+++ b/tests/modules/gatk4/samtofastq/main.nf
@@ -19,3 +19,11 @@ workflow test_gatk4_samtofastq_paired_end {
 
     GATK4_SAMTOFASTQ ( input )
 }
+
+workflow test_gatk4_samtofastq_paired_end_stubs {
+    input = [ [ id:'test', single_end: false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+            ]
+
+    GATK4_SAMTOFASTQ ( input )
+}
diff --git a/tests/modules/gatk4/samtofastq/test.yml b/tests/modules/gatk4/samtofastq/test.yml
index eb25f33b..1288a270 100644
--- a/tests/modules/gatk4/samtofastq/test.yml
+++ b/tests/modules/gatk4/samtofastq/test.yml
@@ -19,3 +19,13 @@
     - path: output/gatk4/test_2.fastq.gz
       md5sum: 613bf64c023609e1c62ad6ce9e4be8d7
     - path: output/gatk4/versions.yml
+
+- name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
+  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
+  tags:
+    - gatk4
+    - gatk4/samtofastq
+  files:
+    - path: output/gatk4/test_1.fastq.gz
+    - path: output/gatk4/test_2.fastq.gz
+    - path: output/gatk4/versions.yml
diff --git a/tests/modules/samtools/view/main.nf b/tests/modules/samtools/view/main.nf
index 9c239066..0e3f597e 100644
--- a/tests/modules/samtools/view/main.nf
+++ b/tests/modules/samtools/view/main.nf
@@ -22,3 +22,12 @@ workflow test_samtools_view_cram {
 
     SAMTOOLS_VIEW ( input, fasta )
 }
+
+workflow test_samtools_view_stubs {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                []
+            ]
+
+    SAMTOOLS_VIEW ( input, [] )
+}
diff --git a/tests/modules/samtools/view/test.yml b/tests/modules/samtools/view/test.yml
index 1287d455..2718130e 100644
--- a/tests/modules/samtools/view/test.yml
+++ b/tests/modules/samtools/view/test.yml
@@ -14,3 +14,11 @@
     - samtools
   files:
     - path: output/samtools/test.cram
+
+- name: samtools view test_samtools_view_stubs
+  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
+  tags:
+    - samtools/view
+    - samtools
+  files:
+    - path: output/samtools/test.bam

From f231291e7730654158cbd3f10b82c292e27fa273 Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 12:58:12 +0200
Subject: [PATCH 20/37] fix gatk4_reversam test

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

diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf
index 162aa0fa..3084658d 100644
--- a/modules/gatk4/revertsam/main.nf
+++ b/modules/gatk4/revertsam/main.nf
@@ -43,7 +43,7 @@ process GATK4_REVERTSAM {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.bam
+    touch ${prefix}.reverted.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From de40c1bf54b79efb4aa2396ded7f8f457cf33c02 Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 13:15:01 +0200
Subject: [PATCH 21/37] chore removing file from test

---
 tests/modules/gatk4/mergebamalignment/main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/modules/gatk4/mergebamalignment/main.nf b/tests/modules/gatk4/mergebamalignment/main.nf
index ebedad9b..0eb6876d 100644
--- a/tests/modules/gatk4/mergebamalignment/main.nf
+++ b/tests/modules/gatk4/mergebamalignment/main.nf
@@ -16,12 +16,12 @@ workflow test_gatk4_mergebamalignment {
 }
 
 workflow test_gatk4_mergebamalignment_stubs {
-    input    = [ [ id:'test' ], // meta map
-                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
-                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
+     input    = [ [ id:'test' ], // meta map
+                 "test_foo.bam",
+                 "test_bar.bam"
                ]
-    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+    fasta    = "genome.fasta"
+    dict     = "genome.fasta.dict"
 
     GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
 }

From 3a4e415fe21982ccb39807d71c16e7d6ad0a1c1a Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 13:30:18 +0200
Subject: [PATCH 22/37] chores adding dummy files for stubs

---
 tests/modules/gatk4/mutect2/main.nf    | 18 +++++++++---------
 tests/modules/gatk4/revertsam/main.nf  |  2 +-
 tests/modules/gatk4/samtofastq/main.nf |  2 +-
 tests/modules/samtools/view/main.nf    |  2 +-
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
index 619d28b8..251e1987 100644
--- a/tests/modules/gatk4/mutect2/main.nf
+++ b/tests/modules/gatk4/mutect2/main.nf
@@ -121,18 +121,18 @@ workflow test_gatk4_mutect2_mitochondria {
 
 workflow test_gatk4_mutect2_tumor_single_stubs {
     input = [ [ id:'test'], // meta map
-              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
-              [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
+              [ "foo.bam" ],
+              [ "foo.bam.bai" ],
               []
             ]
 
-    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
-    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
-    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
-    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
-    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
+    fasta = "genome.fasta"
+    fai = "genome.fasta.fai"
+    dict = "genome.fasta.dict"
+    germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
+    germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
+    panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
+    panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
 
     GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }
diff --git a/tests/modules/gatk4/revertsam/main.nf b/tests/modules/gatk4/revertsam/main.nf
index 5b14d471..738ecd8f 100644
--- a/tests/modules/gatk4/revertsam/main.nf
+++ b/tests/modules/gatk4/revertsam/main.nf
@@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
 
 workflow test_gatk4_revertsam_stubs {
     input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+              "foo_paired_end.bam"
             ]
 
     GATK4_REVERTSAM ( input )
diff --git a/tests/modules/gatk4/samtofastq/main.nf b/tests/modules/gatk4/samtofastq/main.nf
index aad80057..79d04c7c 100644
--- a/tests/modules/gatk4/samtofastq/main.nf
+++ b/tests/modules/gatk4/samtofastq/main.nf
@@ -22,7 +22,7 @@ workflow test_gatk4_samtofastq_paired_end {
 
 workflow test_gatk4_samtofastq_paired_end_stubs {
     input = [ [ id:'test', single_end: false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+              [ "foo_paired_end.bam" ]
             ]
 
     GATK4_SAMTOFASTQ ( input )
diff --git a/tests/modules/samtools/view/main.nf b/tests/modules/samtools/view/main.nf
index 0e3f597e..bdad1078 100644
--- a/tests/modules/samtools/view/main.nf
+++ b/tests/modules/samtools/view/main.nf
@@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
 
 workflow test_samtools_view_stubs {
     input = [ [ id:'test', single_end:false ], // meta map
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                "foo_paired_end.bam",
                 []
             ]
 

From da82e06354c34bf6381a86e5af195b24d7ef98ee Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 14:16:07 +0200
Subject: [PATCH 23/37] fix gatk4_mutect2 test

---
 tests/modules/gatk4/mutect2/main.nf  | 14 +++++++++-----
 tests/modules/gatk4/mutect2/test.yml |  5 +++--
 2 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
index 251e1987..486b78ad 100644
--- a/tests/modules/gatk4/mutect2/main.nf
+++ b/tests/modules/gatk4/mutect2/main.nf
@@ -119,10 +119,14 @@ workflow test_gatk4_mutect2_mitochondria {
     GATK4_MUTECT2_MITO ( input, fasta, fai, dict, [], [], [], [] )
 }
 
-workflow test_gatk4_mutect2_tumor_single_stubs {
-    input = [ [ id:'test'], // meta map
-              [ "foo.bam" ],
-              [ "foo.bam.bai" ],
+workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
+    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
+              [ "foo_parired.bam",
+                "foo_parired2.bam"
+                ],
+              [ "foo_parired.bam.bai",
+                "foo_parired2.bam.bai"
+                ],
               []
             ]
 
@@ -134,5 +138,5 @@ workflow test_gatk4_mutect2_tumor_single_stubs {
     panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
     panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
 
-    GATK4_MUTECT2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
+    GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }
diff --git a/tests/modules/gatk4/mutect2/test.yml b/tests/modules/gatk4/mutect2/test.yml
index 9232cedd..3853801d 100644
--- a/tests/modules/gatk4/mutect2/test.yml
+++ b/tests/modules/gatk4/mutect2/test.yml
@@ -70,12 +70,13 @@
     - path: output/gatk4/test.vcf.gz.tbi
     - path: output/gatk4/versions.yml
 
-- name: gatk4 mutect2 test_gatk4_mutect2_tumor_single_stubs
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_single -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
+- name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
+  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/mutect2
   files:
+    - path: output/gatk4/test.f1r2.tar.gz
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.stats
     - path: output/gatk4/test.vcf.gz.tbi

From ed4dd1a928ebf4308efb720de878045f7773f8e2 Mon Sep 17 00:00:00 2001
From: ljmesi <37740329+ljmesi@users.noreply.github.com>
Date: Mon, 2 May 2022 14:16:12 +0200
Subject: [PATCH 24/37] Add additional handling of fq.gz file name suffix

---
 modules/metaphlan3/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/metaphlan3/main.nf b/modules/metaphlan3/main.nf
index 3fc6b277..bff0eb9a 100644
--- a/modules/metaphlan3/main.nf
+++ b/modules/metaphlan3/main.nf
@@ -23,7 +23,7 @@ process METAPHLAN3 {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input_type  = ("$input".endsWith(".fastq.gz")) ? "--input_type fastq" :  ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
+    def input_type  = ("$input".endsWith(".fastq.gz") || "$input".endsWith(".fq.gz")) ? "--input_type fastq" :  ("$input".contains(".fasta")) ? "--input_type fasta" : ("$input".endsWith(".bowtie2out.txt")) ? "--input_type bowtie2out" : "--input_type sam"
     def input_data  = ("$input_type".contains("fastq")) && !meta.single_end ? "${input[0]},${input[1]}" : "$input"
     def bowtie2_out = "$input_type" == "--input_type bowtie2out" || "$input_type" == "--input_type sam" ? '' : "--bowtie2out ${prefix}.bowtie2out.txt"
 

From 62c6123ec48e15b42bd60b344603a83b658054d8 Mon Sep 17 00:00:00 2001
From: Lucpen <luci9393@hotmail.com>
Date: Mon, 2 May 2022 15:11:57 +0200
Subject: [PATCH 25/37] fix gatk4_mutect2 test by changing main.nf

---
 modules/gatk4/mutect2/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf
index a214b57d..9969ad70 100644
--- a/modules/gatk4/mutect2/main.nf
+++ b/modules/gatk4/mutect2/main.nf
@@ -62,8 +62,8 @@ process GATK4_MUTECT2 {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vcf.gz
-    touch ${prefix}.tbi
-    touch ${prefix}.stats
+    touch ${prefix}.vcf.gz.tbi
+    touch ${prefix}.vcf.gz.stats
     touch ${prefix}.f1r2.tar.gz
 
     cat <<-END_VERSIONS > versions.yml

From 50cc136a7810323f2c802ff3bcc1bf54c85d57a9 Mon Sep 17 00:00:00 2001
From: Lucpen <lucia.pena.perez@scilifelab.se>
Date: Mon, 2 May 2022 15:14:05 +0200
Subject: [PATCH 26/37] Update tests/modules/gatk4/mutect2/main.nf

fix spelling mistake

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
---
 tests/modules/gatk4/mutect2/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
index 486b78ad..310e9ca1 100644
--- a/tests/modules/gatk4/mutect2/main.nf
+++ b/tests/modules/gatk4/mutect2/main.nf
@@ -121,11 +121,11 @@ workflow test_gatk4_mutect2_mitochondria {
 
 workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
     input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
-              [ "foo_parired.bam",
-                "foo_parired2.bam"
+              [ "foo_paired.bam",
+                "foo_paired2.bam"
                 ],
-              [ "foo_parired.bam.bai",
-                "foo_parired2.bam.bai"
+              [ "foo_paired.bam.bai",
+                "foo_paired2.bam.bai"
                 ],
               []
             ]

From b8a59c2b173cf0d987effc8a3e1cd547307a6085 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 3 May 2022 08:20:10 +0200
Subject: [PATCH 27/37] Fixed version annotation

---
 modules/vardictjava/main.nf | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 08318c29..682c26be 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -24,6 +24,8 @@ process VARDICTJAVA {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
+    def VERSION = '1.8.3'
+
     """
     vardict-java \\
         $args \\
@@ -41,7 +43,8 @@ process VARDICTJAVA {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vardict-java: \$(echo 1.8.3)
+        vardict-java: \$VERSION
+        var2vcf_valid.pl: \$(echo \$(var2vcf_valid.pl -h | sed -n 2p | awk '{ print \$2 }'))
     END_VERSIONS
     """
 }

From 9a10e5beb56904061e0b728fea55c8246af74997 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 3 May 2022 08:29:46 +0200
Subject: [PATCH 28/37] Added the missing inputs in meta.yml + correct notation

---
 modules/vardictjava/main.nf               | 10 +++++-----
 modules/vardictjava/meta.yml              | 16 ++++++++++++++--
 tests/modules/vardictjava/nextflow.config |  4 ----
 tests/modules/vardictjava/test.yml        |  2 +-
 4 files changed, 20 insertions(+), 12 deletions(-)

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 682c26be..14964989 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -9,8 +9,8 @@ process VARDICTJAVA {
 
     input:
     tuple val(meta), path(bam), path(bai)
-    path(regions_of_interest)
-    tuple path(reference_fasta), path(reference_fai)
+    path(bed)
+    tuple path(fasta), path(fasta_fai)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -33,8 +33,8 @@ process VARDICTJAVA {
         -b $bam \\
         -th $task.cpus \\
         -N $prefix \\
-        -G $reference_fasta \\
-        $regions_of_interest \\
+        -G $fasta \\
+        $bed \\
         | teststrandbias.R \\
         | var2vcf_valid.pl \\
             $args2 \\
@@ -43,7 +43,7 @@ process VARDICTJAVA {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vardict-java: \$VERSION
+        vardict-java: $VERSION
         var2vcf_valid.pl: \$(echo \$(var2vcf_valid.pl -h | sed -n 2p | awk '{ print \$2 }'))
     END_VERSIONS
     """
diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index e3b2efe7..42480bc1 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -25,17 +25,29 @@ input:
       type: file
       description: BAM/SAM file
       pattern: "*.{bam,sam}"
+  
+  - bai:
+      type: file
+      description: Index of the BAM file 
+      pattern: "*.bai"
 
-  - reference_fasta:
+  - fasta:
       type: file
       description: FASTA of the reference genome
       pattern: "*.{fa,fasta}"
 
-  - regions_of_interest:
+  - fasta_fai:
+      type: file
+      description: The index of the FASTA of the reference genome
+      pattern: "*.fai"
+
+  - bed:
       type: file
       description: BED with the regions of interest
       pattern: "*.bed"
 
+  
+
 output:
   - meta:
       type: map
diff --git a/tests/modules/vardictjava/nextflow.config b/tests/modules/vardictjava/nextflow.config
index e08201cc..50f50a7a 100644
--- a/tests/modules/vardictjava/nextflow.config
+++ b/tests/modules/vardictjava/nextflow.config
@@ -2,8 +2,4 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
     
-    withName: VARDICTJAVA {
-        ext.args = ''
-        ext.args2 = ''
-    }
 }
\ No newline at end of file
diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml
index 549d688e..8cb29c4e 100644
--- a/tests/modules/vardictjava/test.yml
+++ b/tests/modules/vardictjava/test.yml
@@ -6,4 +6,4 @@
     - path: output/vardictjava/test.vcf.gz
       md5sum: 3f1f227afc532bddeb58f16fd3013fc8
     - path: output/vardictjava/versions.yml
-      md5sum: aac455b8c9c9194c5fed80e4fd495b96
+      md5sum: 9b62c431a4f2680412b61c7071bdb1cd

From 71c5d213742b56c62a75b6f34b1f734e073f415e Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 3 May 2022 08:34:12 +0200
Subject: [PATCH 29/37] ran prettier

---
 modules/vardictjava/meta.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 42480bc1..83675fdc 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -25,10 +25,10 @@ input:
       type: file
       description: BAM/SAM file
       pattern: "*.{bam,sam}"
-  
+
   - bai:
       type: file
-      description: Index of the BAM file 
+      description: Index of the BAM file
       pattern: "*.bai"
 
   - fasta:
@@ -46,8 +46,6 @@ input:
       description: BED with the regions of interest
       pattern: "*.bed"
 
-  
-
 output:
   - meta:
       type: map

From d33253513fcd8900db9480450496886ea1f17adb Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 3 May 2022 10:15:30 +0200
Subject: [PATCH 30/37] put the version on top of the file

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

diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf
index 14964989..454b86a4 100644
--- a/modules/vardictjava/main.nf
+++ b/modules/vardictjava/main.nf
@@ -1,3 +1,5 @@
+def VERSION = '1.8.3'
+
 process VARDICTJAVA {
     tag "$meta.id"
     label 'process_medium'
@@ -24,8 +26,6 @@ process VARDICTJAVA {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def VERSION = '1.8.3'
-
     """
     vardict-java \\
         $args \\

From 7c89af359c19131d2f9e8d32bd6ebb0dd682e4d2 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 3 May 2022 10:15:51 +0200
Subject: [PATCH 31/37] Update modules/vardictjava/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/vardictjava/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 83675fdc..63a52611 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -20,7 +20,6 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - bam:
       type: file
       description: BAM/SAM file

From 2dff193b543d78c1176d19c6f9c42385caa131c2 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 3 May 2022 10:15:59 +0200
Subject: [PATCH 32/37] Update modules/vardictjava/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/vardictjava/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 63a52611..a0af9fcc 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -29,7 +29,6 @@ input:
       type: file
       description: Index of the BAM file
       pattern: "*.bai"
-
   - fasta:
       type: file
       description: FASTA of the reference genome

From 3cdbdf50fc6423826e4aeed8fef8e1f75a19f621 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 3 May 2022 10:16:14 +0200
Subject: [PATCH 33/37] Update modules/vardictjava/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/vardictjava/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index a0af9fcc..3afa7e62 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -24,7 +24,6 @@ input:
       type: file
       description: BAM/SAM file
       pattern: "*.{bam,sam}"
-
   - bai:
       type: file
       description: Index of the BAM file

From 1609dfc96dd1ff205f1cac511b8dabb64f8a3db6 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 3 May 2022 10:16:20 +0200
Subject: [PATCH 34/37] Update modules/vardictjava/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/vardictjava/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 3afa7e62..325ce1ca 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -32,7 +32,6 @@ input:
       type: file
       description: FASTA of the reference genome
       pattern: "*.{fa,fasta}"
-
   - fasta_fai:
       type: file
       description: The index of the FASTA of the reference genome

From 01085b3e090b0e64ed0db23a93e00bd891a11639 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 3 May 2022 10:16:30 +0200
Subject: [PATCH 35/37] Update modules/vardictjava/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/vardictjava/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 325ce1ca..5be27690 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -36,7 +36,6 @@ input:
       type: file
       description: The index of the FASTA of the reference genome
       pattern: "*.fai"
-
   - bed:
       type: file
       description: BED with the regions of interest

From 11c6faf433d19803a1a9c198c83bde5ce5ae9706 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 3 May 2022 10:16:36 +0200
Subject: [PATCH 36/37] Update modules/vardictjava/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/vardictjava/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 5be27690..196b090e 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -47,7 +47,6 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - versions:
       type: file
       description: File containing software versions

From 818764128039936e8d94df70427667638b0276a9 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 3 May 2022 10:16:45 +0200
Subject: [PATCH 37/37] Update modules/vardictjava/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/vardictjava/meta.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml
index 196b090e..59fba966 100644
--- a/modules/vardictjava/meta.yml
+++ b/modules/vardictjava/meta.yml
@@ -51,7 +51,6 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
   - vcf:
       type: file
       description: VCF file output