Merge branch 'nf-core:master' into gatk_spark

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
 

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 (optional)
+      pattern: "*.{bed,interval_list}"
   - fasta:
       type: file
       description: The reference FASTA file

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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