From 44e13ae439e0788db8afb227e2801815c459982a Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Tue, 10 May 2022 21:31:43 +0000
Subject: [PATCH 01/18] add module for snippy

---
 modules/snippy/run/main.nf               |  55 ++++++++++++
 modules/snippy/run/meta.yml              | 110 +++++++++++++++++++++++
 tests/config/pytest_modules.yml          |  12 ++-
 tests/modules/snippy/run/main.nf         |  16 ++++
 tests/modules/snippy/run/nextflow.config |   5 ++
 tests/modules/snippy/run/test.yml        |  39 ++++++++
 6 files changed, 233 insertions(+), 4 deletions(-)
 create mode 100644 modules/snippy/run/main.nf
 create mode 100644 modules/snippy/run/meta.yml
 create mode 100644 tests/modules/snippy/run/main.nf
 create mode 100644 tests/modules/snippy/run/nextflow.config
 create mode 100644 tests/modules/snippy/run/test.yml

diff --git a/modules/snippy/run/main.nf b/modules/snippy/run/main.nf
new file mode 100644
index 00000000..73c4b94d
--- /dev/null
+++ b/modules/snippy/run/main.nf
@@ -0,0 +1,55 @@
+process SNIPPY_RUN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2  ':
+        'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }"
+
+    input:
+    tuple val(meta), path(reads)
+    path reference
+
+    output:
+    tuple val(meta), path("${prefix}/${prefix}.tab")              , emit: tab
+    tuple val(meta), path("${prefix}/${prefix}.csv")              , emit: csv
+    tuple val(meta), path("${prefix}/${prefix}.html")             , emit: html
+    tuple val(meta), path("${prefix}/${prefix}.vcf")              , emit: vcf
+    tuple val(meta), path("${prefix}/${prefix}.bed")              , emit: bed
+    tuple val(meta), path("${prefix}/${prefix}.gff")              , emit: gff
+    tuple val(meta), path("${prefix}/${prefix}.bam")              , emit: bam
+    tuple val(meta), path("${prefix}/${prefix}.bam.bai")          , emit: bai
+    tuple val(meta), path("${prefix}/${prefix}.log")              , emit: log
+    tuple val(meta), path("${prefix}/${prefix}.aligned.fa")       , emit: aligned_fa
+    tuple val(meta), path("${prefix}/${prefix}.consensus.fa")     , emit: consensus_fa
+    tuple val(meta), path("${prefix}/${prefix}.consensus.subs.fa"), emit: consensus_subs_fa
+    tuple val(meta), path("${prefix}/${prefix}.raw.vcf")          , emit: raw_vcf
+    tuple val(meta), path("${prefix}/${prefix}.filt.vcf")         , emit: filt_vcf
+    tuple val(meta), path("${prefix}/${prefix}.vcf.gz")           , emit: vcf_gz
+    tuple val(meta), path("${prefix}/${prefix}.vcf.gz.csi")       , emit: vcf_csi
+    tuple val(meta), path("${prefix}/${prefix}.txt")              , emit: txt
+    path "versions.yml"                                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def read_inputs = meta.single_end ? "--se ${reads[0]}" : "--R1 ${reads[0]} --R2 ${reads[1]}"
+    """
+    snippy \\
+        $args \\
+        --cpus $task.cpus \\
+        --outdir $prefix \\
+        --reference $reference \\
+        --prefix $prefix \\
+        $read_inputs
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snippy: \$(echo \$(snippy --version 2>&1) | sed 's/snippy //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/snippy/run/meta.yml b/modules/snippy/run/meta.yml
new file mode 100644
index 00000000..fa176399
--- /dev/null
+++ b/modules/snippy/run/meta.yml
@@ -0,0 +1,110 @@
+name: snippy
+description: Rapid haploid variant calling
+keywords:
+  - variant
+  - fastq
+  - bacteria
+tools:
+  - snippy:
+      description: "Rapid bacterial SNP calling and core genome alignments"
+      homepage: "https://github.com/tseemann/snippy"
+      documentation: "https://github.com/tseemann/snippy"
+      tool_dev_url: "https://github.com/tseemann/snippy"
+      doi: ""
+      licence: "['GPL v2']"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+  - index:
+      type: file
+      description: Reference genome in GenBank (preferred) or FASTA format
+      pattern: "*.{gbk,gbk.gz,fa,fa.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - tab:
+      type: file
+      description: A simple tab-separated summary of all the variants
+      pattern: "*.tab"
+  - csv:
+      type: file
+      description: A comma-separated version of the .tab file
+      pattern: "*.csv"
+  - html:
+      type: file
+      description: A HTML version of the .tab file
+      pattern: "*.html"
+  - vcf:
+      type: file
+      description: The final annotated variants in VCF format
+      pattern: "*.vcf"
+  - bed:
+      type: file
+      description: The variants in BED format
+      pattern: "*.bed"
+  - gff:
+      type: file
+      description: The variants in GFF3 format
+      pattern: "*.gff"
+  - bam:
+      type: file
+      description: The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates.
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: Index for the .bam file
+      pattern: "*.bam.bai"
+  - log:
+      type: file
+      description: A log file with the commands run and their outputs
+      pattern: "*.log"
+  - aligned_fa:
+      type: file
+      description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants)
+      pattern: "*.aligned.fa"
+  - consensus_fa:
+      type: file
+      description: A version of the reference genome with all variants instantiated
+      pattern: "*.consensus.fa"
+  - consensus_subs_fa:
+      type: file
+      description: A version of the reference genome with only substitution variants instantiated
+      pattern: "*.consensus.subs.fa"
+  - raw_vcf:
+      type: file
+      description: The unfiltered variant calls from Freebayes
+      pattern: "*.raw.vcf"
+  - filt_vcf:
+      type: file
+      description: The filtered variant calls from Freebayes
+      pattern: "*.filt.vcf"
+  - vcf_gz:
+      type: file
+      description: Compressed .vcf file via BGZIP
+      pattern: "*.vcf.gz"
+  - vcf_csi:
+      type: file
+      description: 	Index for the .vcf.gz via bcftools index
+      pattern: "*.vcf.gz.csi"
+  - txt:
+      type: file
+      description: Tab-separated columnar list of statistics
+      pattern: "*.txt"
+authors:
+  - "@rpetit3"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 9afe83fd..5a204ac4 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1643,14 +1643,14 @@ samtools/bam2fq:
   - modules/samtools/bam2fq/**
   - tests/modules/samtools/bam2fq/**
 
-samtools/convert:
-  - modules/samtools/convert/**
-  - tests/modules/samtools/convert/**
-
 samtools/collatefastq:
   - modules/samtools/collatefastq/**
   - tests/modules/samtools/collatefastq/**
 
+samtools/convert:
+  - modules/samtools/convert/**
+  - tests/modules/samtools/convert/**
+
 samtools/depth:
   - modules/samtools/depth/**
   - tests/modules/samtools/depth/**
@@ -1787,6 +1787,10 @@ snapaligner/index:
   - modules/snapaligner/index/**
   - tests/modules/snapaligner/index/**
 
+snippy/run:
+  - modules/snippy/run/**
+  - tests/modules/snippy/run/**
+
 snpdists:
   - modules/snpdists/**
   - tests/modules/snpdists/**
diff --git a/tests/modules/snippy/run/main.nf b/tests/modules/snippy/run/main.nf
new file mode 100644
index 00000000..bfc4082e
--- /dev/null
+++ b/tests/modules/snippy/run/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNIPPY_RUN } from '../../../../modules/snippy/run/main.nf'
+
+workflow test_snippy_run {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    SNIPPY_RUN ( input, reference )
+}
diff --git a/tests/modules/snippy/run/nextflow.config b/tests/modules/snippy/run/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/snippy/run/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/snippy/run/test.yml b/tests/modules/snippy/run/test.yml
new file mode 100644
index 00000000..e38e8b9e
--- /dev/null
+++ b/tests/modules/snippy/run/test.yml
@@ -0,0 +1,39 @@
+- name: snippy run test_snippy_run
+  command: nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config
+  tags:
+    - snippy
+    - snippy/run
+  files:
+    - path: output/snippy/test/test.aligned.fa
+      md5sum: 47e3390d4167edf1955d162d37aca5e3
+    - path: output/snippy/test/test.bam
+    - path: output/snippy/test/test.bam.bai
+    - path: output/snippy/test/test.bed
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/snippy/test/test.consensus.fa
+      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
+    - path: output/snippy/test/test.consensus.subs.fa
+      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
+    - path: output/snippy/test/test.csv
+      md5sum: 322f942115e5945c2041a88246166703
+    - path: output/snippy/test/test.filt.vcf
+      contains: ['fileformat', 'freebayes', 'CHROM']
+    - path: output/snippy/test/test.gff
+      md5sum: df19e1b84ba6f691d20c72b397c88abf
+    - path: output/snippy/test/test.html
+      md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938
+    - path: output/snippy/test/test.log
+      contains: ['snippy', 'consensus', 'subs']
+    - path: output/snippy/test/test.raw.vcf
+      contains: ['fileformat', 'freebayes', 'CHROM']
+    - path: output/snippy/test/test.tab
+      md5sum: beb9bde3bce985e53e8feba9ec5b136e
+    - path: output/snippy/test/test.txt
+      contains: ['DateTime', 'ReadFiles', 'VariantTotal']
+    - path: output/snippy/test/test.vcf
+      contains: ['fileformat', 'freebayes', 'CHROM']
+    - path: output/snippy/test/test.vcf.gz
+    - path: output/snippy/test/test.vcf.gz.csi
+      md5sum: bed9fa291c220a1ba04eb2d448932ffc
+    - path: output/snippy/versions.yml
+      md5sum: 518aad56c4dbefb6cbcde5ab38cf7b5d

From f15848d4774f095f43594516769fde889a7a3d12 Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Tue, 10 May 2022 21:44:40 +0000
Subject: [PATCH 02/18] fix typo

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

diff --git a/modules/snippy/run/meta.yml b/modules/snippy/run/meta.yml
index fa176399..13c923d8 100644
--- a/modules/snippy/run/meta.yml
+++ b/modules/snippy/run/meta.yml
@@ -100,7 +100,7 @@ output:
       pattern: "*.vcf.gz"
   - vcf_csi:
       type: file
-      description: 	Index for the .vcf.gz via bcftools index
+      description: Index for the .vcf.gz via bcftools index
       pattern: "*.vcf.gz.csi"
   - txt:
       type: file

From 56e94f625e69e48de7c218b79857cc3a59cb9220 Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Tue, 10 May 2022 21:47:11 +0000
Subject: [PATCH 03/18] remove empty file md5

---
 tests/modules/snippy/run/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/snippy/run/test.yml b/tests/modules/snippy/run/test.yml
index e38e8b9e..ac945e88 100644
--- a/tests/modules/snippy/run/test.yml
+++ b/tests/modules/snippy/run/test.yml
@@ -9,7 +9,6 @@
     - path: output/snippy/test/test.bam
     - path: output/snippy/test/test.bam.bai
     - path: output/snippy/test/test.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/snippy/test/test.consensus.fa
       md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
     - path: output/snippy/test/test.consensus.subs.fa

From ef2996e4a5f4f74b4b49bbbd308c3142de8d894d Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Tue, 10 May 2022 21:47:57 +0000
Subject: [PATCH 04/18] match names in meta and main

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

diff --git a/modules/snippy/run/meta.yml b/modules/snippy/run/meta.yml
index 13c923d8..2eb008a1 100644
--- a/modules/snippy/run/meta.yml
+++ b/modules/snippy/run/meta.yml
@@ -1,4 +1,4 @@
-name: snippy
+name: snippy_run
 description: Rapid haploid variant calling
 keywords:
   - variant

From 7ced6e20de5a69a25fb57b00244a49329709186a Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Wed, 11 May 2022 18:00:36 +0000
Subject: [PATCH 05/18] make prettier

---
 tests/modules/snippy/run/test.yml | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/tests/modules/snippy/run/test.yml b/tests/modules/snippy/run/test.yml
index ac945e88..10e24f55 100644
--- a/tests/modules/snippy/run/test.yml
+++ b/tests/modules/snippy/run/test.yml
@@ -1,8 +1,9 @@
 - name: snippy run test_snippy_run
-  command: nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config
+  command: |
+    nextflow run tests/modules/snippy/run -entry test_snippy_run -c tests/config/nextflow.config -c tests/modules/snippy/run/nextflow.config
   tags:
-    - snippy
     - snippy/run
+    - snippy
   files:
     - path: output/snippy/test/test.aligned.fa
       md5sum: 47e3390d4167edf1955d162d37aca5e3
@@ -16,21 +17,21 @@
     - path: output/snippy/test/test.csv
       md5sum: 322f942115e5945c2041a88246166703
     - path: output/snippy/test/test.filt.vcf
-      contains: ['fileformat', 'freebayes', 'CHROM']
+      contains: ["fileformat", "freebayes", "CHROM"]
     - path: output/snippy/test/test.gff
       md5sum: df19e1b84ba6f691d20c72b397c88abf
     - path: output/snippy/test/test.html
       md5sum: 1ccbf0ffcadae1a6b2e11681d24c9938
     - path: output/snippy/test/test.log
-      contains: ['snippy', 'consensus', 'subs']
+      contains: ["snippy", "consensus", "subs"]
     - path: output/snippy/test/test.raw.vcf
-      contains: ['fileformat', 'freebayes', 'CHROM']
+      contains: ["fileformat", "freebayes", "CHROM"]
     - path: output/snippy/test/test.tab
       md5sum: beb9bde3bce985e53e8feba9ec5b136e
     - path: output/snippy/test/test.txt
-      contains: ['DateTime', 'ReadFiles', 'VariantTotal']
+      contains: ["DateTime", "ReadFiles", "VariantTotal"]
     - path: output/snippy/test/test.vcf
-      contains: ['fileformat', 'freebayes', 'CHROM']
+      contains: ["fileformat", "freebayes", "CHROM"]
     - path: output/snippy/test/test.vcf.gz
     - path: output/snippy/test/test.vcf.gz.csi
       md5sum: bed9fa291c220a1ba04eb2d448932ffc

From 63db63757cab03cfa7a02c0d0f134b66fbfadea6 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Mon, 30 May 2022 10:15:40 +0200
Subject: [PATCH 06/18] bump picard versions

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

diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf
index fd102f67..aff83c9f 100644
--- a/modules/picard/addorreplacereadgroups/main.nf
+++ b/modules/picard/addorreplacereadgroups/main.nf
@@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf
index 62989565..0042c3f1 100644
--- a/modules/picard/cleansam/main.nf
+++ b/modules/picard/cleansam/main.nf
@@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index 06b6b8f3..52d5c84a 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index 3c3152df..6fe9881b 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index cab1fe0c..e231afe2 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf
index 2348c496..16a5ff19 100644
--- a/modules/picard/createsequencedictionary/main.nf
+++ b/modules/picard/createsequencedictionary/main.nf
@@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/picard/crosscheckfingerprints/main.nf b/modules/picard/crosscheckfingerprints/main.nf
index d3b59402..c7c4766c 100644
--- a/modules/picard/crosscheckfingerprints/main.nf
+++ b/modules/picard/crosscheckfingerprints/main.nf
@@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input1)
diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf
index adedcdc2..e17c4686 100644
--- a/modules/picard/filtersamreads/main.nf
+++ b/modules/picard/filtersamreads/main.nf
@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)
diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf
index 539b1082..616acce8 100644
--- a/modules/picard/fixmateinformation/main.nf
+++ b/modules/picard/fixmateinformation/main.nf
@@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf
index c92abfeb..a82f1466 100644
--- a/modules/picard/liftovervcf/main.nf
+++ b/modules/picard/liftovervcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index 1565c647..87f913d4 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index 1e32c63a..d65f518c 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf
index cee60fd1..5e09d907 100644
--- a/modules/picard/sortsam/main.nf
+++ b/modules/picard/sortsam/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf
index fb8dbb79..8f886393 100644
--- a/modules/picard/sortvcf/main.nf
+++ b/modules/picard/sortvcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTVCF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.2--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)

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 07/18] 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 08/18] 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 09/18] 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"

From b4b1f3b81d897b97da0655cf48107b70aa4b2f73 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 2 Jun 2022 16:20:12 +0200
Subject: [PATCH 10/18] add intervals to calibratedragstrmodel

---
 modules/gatk4/calibratedragstrmodel/main.nf   |  4 ++-
 modules/gatk4/calibratedragstrmodel/meta.yml  |  4 +++
 .../gatk4/calibratedragstrmodel/main.nf       | 26 +++++++++++++++++--
 .../gatk4/calibratedragstrmodel/test.yml      | 13 ++++++++--
 4 files changed, 42 insertions(+), 5 deletions(-)

diff --git a/modules/gatk4/calibratedragstrmodel/main.nf b/modules/gatk4/calibratedragstrmodel/main.nf
index 00a11de0..08ba7008 100644
--- a/modules/gatk4/calibratedragstrmodel/main.nf
+++ b/modules/gatk4/calibratedragstrmodel/main.nf
@@ -8,7 +8,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
         'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bam_index)
+    tuple val(meta), path(bam), path(bam_index), path(intervals)
     path  fasta
     path  fasta_fai
     path  dict
@@ -24,6 +24,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals_command = intervals ? "--intervals $intervals" : ""
 
     def avail_mem = 3
     if (!task.memory) {
@@ -37,6 +38,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
         --output ${prefix}.txt \\
         --reference $fasta \\
         --str-table-path $strtablefile \\
+        $intervals_command \\
         --tmp-dir . \\
         $args
 
diff --git a/modules/gatk4/calibratedragstrmodel/meta.yml b/modules/gatk4/calibratedragstrmodel/meta.yml
index e6d2b0b1..c3c40d81 100644
--- a/modules/gatk4/calibratedragstrmodel/meta.yml
+++ b/modules/gatk4/calibratedragstrmodel/meta.yml
@@ -33,6 +33,10 @@ input:
       type: file
       description: index of the BAM/CRAM/SAM file
       pattern: "*.{bai,crai,sai}"
+  - intervals:
+      type: file
+      description: BED file or interval list containing regions
+      pattern: "*.{bed,interval_list}"
   - fasta:
       type: file
       description: The reference FASTA file
diff --git a/tests/modules/gatk4/calibratedragstrmodel/main.nf b/tests/modules/gatk4/calibratedragstrmodel/main.nf
index 4d4e9896..136a9742 100644
--- a/tests/modules/gatk4/calibratedragstrmodel/main.nf
+++ b/tests/modules/gatk4/calibratedragstrmodel/main.nf
@@ -9,7 +9,8 @@ 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)
+        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)
@@ -28,7 +29,28 @@ 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)
+        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 )
+}
+
+workflow test_gatk4_calibratedragstrmodel_beds {
+    
+    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),
+        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
     ]
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
diff --git a/tests/modules/gatk4/calibratedragstrmodel/test.yml b/tests/modules/gatk4/calibratedragstrmodel/test.yml
index bc46dead..53c428a9 100644
--- a/tests/modules/gatk4/calibratedragstrmodel/test.yml
+++ b/tests/modules/gatk4/calibratedragstrmodel/test.yml
@@ -1,8 +1,8 @@
 - 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
+    - gatk4
   files:
     - path: output/gatk4/test.txt
       md5sum: 0a1a1583b157fa2251dd931ed165da4f
@@ -10,8 +10,17 @@
 - 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
+    - gatk4
   files:
     - path: output/gatk4/test.txt
       md5sum: 1aa7ab38023f724877b3323c5e6b9a4e
+
+- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds
+  command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_beds -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
+  tags:
+    - gatk4/calibratedragstrmodel
+    - gatk4
+  files:
+    - path: output/gatk4/test.txt
+      md5sum: def8baccad7bd59006f08fcb0a6721bf

From f3c0107fa2ecdc510b4f569dc3e062c7e028ac7a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Thu, 2 Jun 2022 16:24:03 +0200
Subject: [PATCH 11/18] added optional to intervals

---
 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 c3c40d81..e71dac5e 100644
--- a/modules/gatk4/calibratedragstrmodel/meta.yml
+++ b/modules/gatk4/calibratedragstrmodel/meta.yml
@@ -35,7 +35,7 @@ input:
       pattern: "*.{bai,crai,sai}"
   - intervals:
       type: file
-      description: BED file or interval list containing regions
+      description: BED file or interval list containing regions (optional)
       pattern: "*.{bed,interval_list}"
   - fasta:
       type: file

From 544b62df45d3043ca2c5ca3a131284fe0d74026b Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 2 Jun 2022 21:11:17 +0200
Subject: [PATCH 12/18] Star work on GATK UG

---
 modules/gatk/unifiedgenotyper/main.nf         | 50 ++++++++++++++++++
 modules/gatk/unifiedgenotyper/meta.yml        | 51 +++++++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/modules/gatk/unifiedgenotyper/main.nf   | 15 ++++++
 .../gatk/unifiedgenotyper/nextflow.config     |  5 ++
 tests/modules/gatk/unifiedgenotyper/test.yml  | 14 +++++
 6 files changed, 139 insertions(+)
 create mode 100644 modules/gatk/unifiedgenotyper/main.nf
 create mode 100644 modules/gatk/unifiedgenotyper/meta.yml
 create mode 100644 tests/modules/gatk/unifiedgenotyper/main.nf
 create mode 100644 tests/modules/gatk/unifiedgenotyper/nextflow.config
 create mode 100644 tests/modules/gatk/unifiedgenotyper/test.yml

diff --git a/modules/gatk/unifiedgenotyper/main.nf b/modules/gatk/unifiedgenotyper/main.nf
new file mode 100644
index 00000000..4dd6e408
--- /dev/null
+++ b/modules/gatk/unifiedgenotyper/main.nf
@@ -0,0 +1,50 @@
+process GATK_UNIFIEDGENOTYPER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
+        'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
+
+    input:
+    tuple val(meta), path(input), path(index)
+    path(fasta)
+    path(fai)
+    path(dict)
+    path(known_vcf)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK RealignerTargetCreator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+
+    """
+    gatk3 \\
+        -Xmx${avail_mem}g \\
+        -nt ${task.cpus} \\
+        -T UnifiedGenotyper \\
+        -I ${input} \\
+        -R ${fasta} \\
+        -o ${prefix}.vcf \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/gatk/unifiedgenotyper/meta.yml b/modules/gatk/unifiedgenotyper/meta.yml
new file mode 100644
index 00000000..7a992591
--- /dev/null
+++ b/modules/gatk/unifiedgenotyper/meta.yml
@@ -0,0 +1,51 @@
+name: "gatk_unifiedgenotyper"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "gatk":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      doi: ""
+      licence: "['BSD', 'https://www.broadinstitute.org/gatk/about/#licensing', 'https://software.broadinstitute.org/gatk/download/licensing']"
+
+## 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:
+  - "@jfy133"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index d4bfac5b..0d3a21c2 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -715,6 +715,10 @@ gamma/gamma:
   - modules/gamma/gamma/**
   - tests/modules/gamma/gamma/**
 
+gatk/unifiedgenotyper:
+  - modules/gatk/unifiedgenotyper/**
+  - tests/modules/gatk/unifiedgenotyper/**
+
 gatk4/applybqsr:
   - modules/gatk4/applybqsr/**
   - tests/modules/gatk4/applybqsr/**
diff --git a/tests/modules/gatk/unifiedgenotyper/main.nf b/tests/modules/gatk/unifiedgenotyper/main.nf
new file mode 100644
index 00000000..86a23790
--- /dev/null
+++ b/tests/modules/gatk/unifiedgenotyper/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/gatk/unifiedgenotyper/main.nf'
+
+workflow test_gatk_unifiedgenotyper {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    GATK_UNIFIEDGENOTYPER ( input )
+}
diff --git a/tests/modules/gatk/unifiedgenotyper/nextflow.config b/tests/modules/gatk/unifiedgenotyper/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/gatk/unifiedgenotyper/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/gatk/unifiedgenotyper/test.yml b/tests/modules/gatk/unifiedgenotyper/test.yml
new file mode 100644
index 00000000..aad9aec9
--- /dev/null
+++ b/tests/modules/gatk/unifiedgenotyper/test.yml
@@ -0,0 +1,14 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml gatk/unifiedgenotyper
+- name: "gatk unifiedgenotyper"
+  command: nextflow run ./tests/modules/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config -c ./tests/modules/gatk/unifiedgenotyper/nextflow.config
+  tags:
+    - "gatk"
+    #
+    - "gatk/unifiedgenotyper"
+    #
+  files:
+    - path: "output/gatk/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/gatk/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b

From a14855dbe8648ca445759f57a1a2805ec4812615 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 2 Jun 2022 21:22:21 +0200
Subject: [PATCH 13/18] Start meta

---
 modules/gatk/unifiedgenotyper/main.nf  | 16 ++++++-
 modules/gatk/unifiedgenotyper/meta.yml | 59 ++++++++++++++++----------
 2 files changed, 51 insertions(+), 24 deletions(-)

diff --git a/modules/gatk/unifiedgenotyper/main.nf b/modules/gatk/unifiedgenotyper/main.nf
index 4dd6e408..896a347e 100644
--- a/modules/gatk/unifiedgenotyper/main.nf
+++ b/modules/gatk/unifiedgenotyper/main.nf
@@ -13,9 +13,13 @@ process GATK_UNIFIEDGENOTYPER {
     path(fai)
     path(dict)
     path(known_vcf)
+    path(intervals)
+    path(contamination)
+    path(dbsnps)
+    path(comp)
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
     path "versions.yml"           , emit: versions
 
     when:
@@ -24,6 +28,10 @@ process GATK_UNIFIEDGENOTYPER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def contamination_file = contamination ? "-contaminationFile ${contamination}" : ""
+    def dbsnps_file = dbsnps ? "--dbsnp ${dbsnps}" : ""
+    def comp_file = comp ? "--comp ${comp}" : ""
+    def intervals_file = intervals ? "--intervals ${intervals}" : ""
 
     def avail_mem = 3
     if (!task.memory) {
@@ -39,9 +47,15 @@ process GATK_UNIFIEDGENOTYPER {
         -T UnifiedGenotyper \\
         -I ${input} \\
         -R ${fasta} \\
+        ${contamination_file} \\
+        ${dbsnps_file} \\
+        ${comp_file} \\
+        ${intervals_file}
         -o ${prefix}.vcf \\
         $args
 
+    gzip -n *.vcf
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gatk: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
diff --git a/modules/gatk/unifiedgenotyper/meta.yml b/modules/gatk/unifiedgenotyper/meta.yml
index 7a992591..5f85c451 100644
--- a/modules/gatk/unifiedgenotyper/meta.yml
+++ b/modules/gatk/unifiedgenotyper/meta.yml
@@ -1,51 +1,64 @@
 name: "gatk_unifiedgenotyper"
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
 keywords:
-  - sort
+  - bam
+  - vcf
+  - variant calling
+  - indel
+  - realignment
+  - targets
 tools:
   - "gatk":
-      ## TODO nf-core: Add a description and other details for the software below
       description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
-      homepage: "None"
-      documentation: "None"
-      tool_dev_url: "None"
-      doi: ""
-      licence: "['BSD', 'https://www.broadinstitute.org/gatk/about/#licensing', 'https://software.broadinstitute.org/gatk/download/licensing']"
+      homepage: "https://gatk.broadinstitute.org/hc/en-us"
+      documentation: "https://github.com/broadinstitute/gatk-docs"
+      licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
 
-## 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:
+  - input:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: Sorted and indexed BAM/CRAM/SAM file
+      pattern: "*.bam"
+  - index:
+      type: file
+      description: BAM index file
+      pattern: "*.bai"
+  - fasta:
+      type: file
+      description: Reference file used to generate BAM file
+      pattern: ".{fasta,fa,fna}"
+  - fai:
+      type: file
+      description: Index of reference file used to generate BAM file
+      pattern: ".fai"
+  - dict:
+      type: file
+      description: GATK dict file for reference
+      pattern: ".dict"
+  - known_vcf:
+      type: file
+      description: Optional input VCF file(s) with known indels
+      pattern: ".vcf"
 
-## 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:
+  - vcf:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: VCF file containing called variants
+      pattern: "*.vcf.gz"
 
 authors:
+  - "@ilight1542"
   - "@jfy133"

From a565d9072aba07b369c6e3c43f4168556d32678c Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 2 Jun 2022 21:39:39 +0200
Subject: [PATCH 14/18] Add GATK UnifiedGenotyper

---
 modules/gatk/unifiedgenotyper/main.nf        | 13 ++++++------
 modules/gatk/unifiedgenotyper/meta.yml       | 21 ++++++++++++++------
 tests/modules/gatk/unifiedgenotyper/main.nf  | 15 ++++++++------
 tests/modules/gatk/unifiedgenotyper/test.yml | 19 +++++++-----------
 4 files changed, 37 insertions(+), 31 deletions(-)

diff --git a/modules/gatk/unifiedgenotyper/main.nf b/modules/gatk/unifiedgenotyper/main.nf
index 896a347e..47d83def 100644
--- a/modules/gatk/unifiedgenotyper/main.nf
+++ b/modules/gatk/unifiedgenotyper/main.nf
@@ -12,15 +12,14 @@ process GATK_UNIFIEDGENOTYPER {
     path(fasta)
     path(fai)
     path(dict)
-    path(known_vcf)
     path(intervals)
     path(contamination)
-    path(dbsnps)
+    path(dbsnp)
     path(comp)
 
     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
@@ -29,7 +28,7 @@ process GATK_UNIFIEDGENOTYPER {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def contamination_file = contamination ? "-contaminationFile ${contamination}" : ""
-    def dbsnps_file = dbsnps ? "--dbsnp ${dbsnps}" : ""
+    def dbsnp_file = dbsnp ? "--dbsnp ${dbsnp}" : ""
     def comp_file = comp ? "--comp ${comp}" : ""
     def intervals_file = intervals ? "--intervals ${intervals}" : ""
 
@@ -48,9 +47,9 @@ process GATK_UNIFIEDGENOTYPER {
         -I ${input} \\
         -R ${fasta} \\
         ${contamination_file} \\
-        ${dbsnps_file} \\
+        ${dbsnp_file} \\
         ${comp_file} \\
-        ${intervals_file}
+        ${intervals_file} \\
         -o ${prefix}.vcf \\
         $args
 
@@ -58,7 +57,7 @@ process GATK_UNIFIEDGENOTYPER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gatk: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        gatk: \$(echo \$(gatk3 --version))
     END_VERSIONS
     """
 }
diff --git a/modules/gatk/unifiedgenotyper/meta.yml b/modules/gatk/unifiedgenotyper/meta.yml
index 5f85c451..e414d146 100644
--- a/modules/gatk/unifiedgenotyper/meta.yml
+++ b/modules/gatk/unifiedgenotyper/meta.yml
@@ -3,9 +3,6 @@ keywords:
   - bam
   - vcf
   - variant calling
-  - indel
-  - realignment
-  - targets
 tools:
   - "gatk":
       description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
@@ -39,10 +36,22 @@ input:
       type: file
       description: GATK dict file for reference
       pattern: ".dict"
-  - known_vcf:
+  - intervals:
       type: file
-      description: Optional input VCF file(s) with known indels
-      pattern: ".vcf"
+      description: Bed file with the genomic regions included in the library (optional)
+      pattern: "*.intervals"
+  - contamination:
+      type: file
+      description: Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove
+      pattern: "*"
+  - dbsnps:
+      type: file
+      description: VCF file containing known sites (optional)
+      pattern: "*"
+  - comp:
+      type: file
+      description: Comparison VCF file (optional)
+      pattern: "*"
 
 output:
   - meta:
diff --git a/tests/modules/gatk/unifiedgenotyper/main.nf b/tests/modules/gatk/unifiedgenotyper/main.nf
index 86a23790..6d145e76 100644
--- a/tests/modules/gatk/unifiedgenotyper/main.nf
+++ b/tests/modules/gatk/unifiedgenotyper/main.nf
@@ -5,11 +5,14 @@ nextflow.enable.dsl = 2
 include { GATK_UNIFIEDGENOTYPER } from '../../../../modules/gatk/unifiedgenotyper/main.nf'
 
 workflow test_gatk_unifiedgenotyper {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
-    ]
 
-    GATK_UNIFIEDGENOTYPER ( input )
+    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)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
 }
diff --git a/tests/modules/gatk/unifiedgenotyper/test.yml b/tests/modules/gatk/unifiedgenotyper/test.yml
index aad9aec9..498e7991 100644
--- a/tests/modules/gatk/unifiedgenotyper/test.yml
+++ b/tests/modules/gatk/unifiedgenotyper/test.yml
@@ -1,14 +1,9 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml gatk/unifiedgenotyper
-- name: "gatk unifiedgenotyper"
-  command: nextflow run ./tests/modules/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config -c ./tests/modules/gatk/unifiedgenotyper/nextflow.config
+- name: gatk unifiedgenotyper test_gatk_unifiedgenotyper
+  command: nextflow run ./tests/modules/gatk/unifiedgenotyper -entry test_gatk_unifiedgenotyper -c ./tests/config/nextflow.config  -c ./tests/modules/gatk/unifiedgenotyper/nextflow.config
   tags:
-    - "gatk"
-    #
-    - "gatk/unifiedgenotyper"
-    #
+    - gatk
+    - gatk/unifiedgenotyper
   files:
-    - path: "output/gatk/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
-    - path: output/gatk/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+    - path: output/gatk/test.vcf.gz
+      contains:
+        - "#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test"

From d7cec801b244d8aa0a98aa94934b191ed5720f92 Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Fri, 3 Jun 2022 13:05:43 -0600
Subject: [PATCH 15/18] Update main.nf

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

diff --git a/modules/snippy/run/main.nf b/modules/snippy/run/main.nf
index 73c4b94d..5ecdbea8 100644
--- a/modules/snippy/run/main.nf
+++ b/modules/snippy/run/main.nf
@@ -4,7 +4,7 @@ process SNIPPY_RUN {
 
     conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2  ':
+        'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2' :
         'quay.io/biocontainers/snippy:4.6.0--hdfd78af_2' }"
 
     input:

From e827a042ce1f55a37a8e771944b566faa5108e8e Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 3 Jun 2022 21:24:03 +0200
Subject: [PATCH 16/18] Update modules/gatk/unifiedgenotyper/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
---
 modules/gatk/unifiedgenotyper/main.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/gatk/unifiedgenotyper/main.nf b/modules/gatk/unifiedgenotyper/main.nf
index 47d83def..e88ac7c5 100644
--- a/modules/gatk/unifiedgenotyper/main.nf
+++ b/modules/gatk/unifiedgenotyper/main.nf
@@ -9,13 +9,13 @@ process GATK_UNIFIEDGENOTYPER {
 
     input:
     tuple val(meta), path(input), path(index)
-    path(fasta)
-    path(fai)
-    path(dict)
-    path(intervals)
-    path(contamination)
-    path(dbsnp)
-    path(comp)
+    path  fasta
+    path  fai
+    path  dict
+    path  intervals
+    path  contamination
+    path  dbsnp
+    path  comp
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf

From 771425e7a050acf0e1be41d9e6fc800f675c3e58 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 7 Jun 2022 12:11:18 +0200
Subject: [PATCH 17/18] add threads to calibratedragstrmodel

---
 modules/gatk4/calibratedragstrmodel/main.nf        |  1 +
 tests/modules/gatk4/calibratedragstrmodel/test.yml | 12 ++++++------
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/modules/gatk4/calibratedragstrmodel/main.nf b/modules/gatk4/calibratedragstrmodel/main.nf
index 08ba7008..b4e47edc 100644
--- a/modules/gatk4/calibratedragstrmodel/main.nf
+++ b/modules/gatk4/calibratedragstrmodel/main.nf
@@ -38,6 +38,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
         --output ${prefix}.txt \\
         --reference $fasta \\
         --str-table-path $strtablefile \\
+        --threads $task.cpus \\
         $intervals_command \\
         --tmp-dir . \\
         $args
diff --git a/tests/modules/gatk4/calibratedragstrmodel/test.yml b/tests/modules/gatk4/calibratedragstrmodel/test.yml
index 53c428a9..285d04ca 100644
--- a/tests/modules/gatk4/calibratedragstrmodel/test.yml
+++ b/tests/modules/gatk4/calibratedragstrmodel/test.yml
@@ -1,26 +1,26 @@
 - 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/calibratedragstrmodel
     - gatk4
+    - gatk4/calibratedragstrmodel
   files:
     - path: output/gatk4/test.txt
-      md5sum: 0a1a1583b157fa2251dd931ed165da4f
+      md5sum: e16fa32906c74bb18b93e98a86718ff1
 
 - 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/calibratedragstrmodel
     - gatk4
+    - gatk4/calibratedragstrmodel
   files:
     - path: output/gatk4/test.txt
-      md5sum: 1aa7ab38023f724877b3323c5e6b9a4e
+      md5sum: 81c7bf338886cb4d5c2cc07fc56afe44
 
 - name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds
   command: nextflow run ./tests/modules/gatk4/calibratedragstrmodel -entry test_gatk4_calibratedragstrmodel_beds -c ./tests/config/nextflow.config  -c ./tests/modules/gatk4/calibratedragstrmodel/nextflow.config
   tags:
-    - gatk4/calibratedragstrmodel
     - gatk4
+    - gatk4/calibratedragstrmodel
   files:
     - path: output/gatk4/test.txt
-      md5sum: def8baccad7bd59006f08fcb0a6721bf
+      md5sum: cb6a9acdee042302b54fd1f59b5f54ee

From 4c7ef30fb64f75ba4499d3b8fba24a068b1ce586 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 7 Jun 2022 12:17:14 +0200
Subject: [PATCH 18/18] changed to label to medium

---
 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 b4e47edc..37a54de4 100644
--- a/modules/gatk4/calibratedragstrmodel/main.nf
+++ b/modules/gatk4/calibratedragstrmodel/main.nf
@@ -1,6 +1,6 @@
 process GATK4_CALIBRATEDRAGSTRMODEL {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?