bump picard (nf-core#3966)

* bump picard * fix linting * fix subwf * fix module * fix linting * omit conda test for bam_qc_picard * omit conda tests for hsmetrics and wgsmetrics
adamrtalbot · Oct 16, 2023 · b7523a2 · b7523a2
1 parent b3149fb
commit b7523a2
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Showing 24 changed files with 88 additions and 100 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -214,6 +214,10 @@ jobs:
             tags: parabricks/applybqsr
           - profile: "conda"
             tags: parabricks/fq2bam
+          - profile: "conda"
+            tags: picard/collecthsmetrics
+          - profile: "conda"
+            tags: picard/collectwgsmetrics
           - profile: "conda"
             tags: scimap/mcmicro
           - profile: "conda"
@@ -264,6 +268,8 @@ jobs:
             tags: subworkflows/fasta_clean_fcs
           - profile: "conda"
             tags: islandpath
+          - profile: "conda"
+            tags: subworkflows/bam_qc_picard
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}

diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf
@@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf
@@ -2,10 +2,10 @@ process PICARD_BEDTOINTERVALLIST {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bed)

diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf
@@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(bait_intervals), path(target_intervals)

diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTINSERTSIZEMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bam), path(bai)

diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTRNASEQMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0 r::r-base"
+    conda "bioconda::picard=3.1.0 r::r-base"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf
@@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf
@@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input1)

diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf
@@ -2,10 +2,10 @@ process PICARD_FASTQTOSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf
@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)

diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf
@@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)

diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf
@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)

diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf
@@ -3,10 +3,10 @@ process PICARD_RENAMESAMPLEINVCF {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)

diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml
@@ -3,6 +3,7 @@ description: changes name of sample in the vcf file
 keywords:
   - picard
   - picard/renamesampleinvcf
+  - vcf
 tools:
   - "picard":
       description: |

diff --git a/modules/nf-core/picard/scatterintervalsbyns/main.nf b/modules/nf-core/picard/scatterintervalsbyns/main.nf
@@ -2,10 +2,10 @@ process PICARD_SCATTERINTERVALSBYNS {
     tag "$fasta"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTVCF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)

diff --git a/tests/modules/nf-core/picard/markduplicates/test.yml b/tests/modules/nf-core/picard/markduplicates/test.yml
@@ -1,57 +1,38 @@
 - name: picard markduplicates test_picard_markduplicates_sorted_bam
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config
   tags:
-    - picard/markduplicates
     - picard
+    - picard/markduplicates
   files:
     - path: output/picard/test.marked.MarkDuplicates.metrics.txt
       contains:
         - "1.0	97	97"
     - path: output/picard/test.marked.bam
-      md5sum: 9963cba5c95a8d5cb632df217aa40d63
-    - path: output/picard/versions.yml
-- name: picard markduplicates test_picard_markduplicates_sorted_bam stub
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config -stub-run
-  tags:
-    - picard/markduplicates
-    - picard
-  files:
-    - path: output/picard/test.marked.MarkDuplicates.metrics.txt
-    - path: output/picard/test.marked.bam
+      md5sum: 41a9a8cbe2400fb8307ce1a7899e19b6
     - path: output/picard/versions.yml
+
 - name: picard markduplicates test_picard_markduplicates_unsorted_bam
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config
   tags:
-    - picard/markduplicates
     - picard
+    - picard/markduplicates
   files:
     - path: output/picard/test.marked.MarkDuplicates.metrics.txt
       contains:
         - "1.0	97	97"
-    - path: ./output/picard/test.marked.bam
-- name: picard markduplicates test_picard_markduplicates_unsorted_bam stub
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config -stub-run
+    - path: output/picard/test.marked.bam
+      md5sum: 6552e40d42a77bcec9f184b076e89340
+    - path: output/picard/versions.yml
+
+- name: picard markduplicates test_picard_markduplicates_sorted_cram
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_cram -c ./tests/config/nextflow.config
   tags:
-    - picard/markduplicates
     - picard
-  files:
-    - path: output/picard/test.marked.MarkDuplicates.metrics.txt
-    - path: ./output/picard/test.marked.bam
-- name: picard markduplicates sorted cram
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
-  tags:
     - picard/markduplicates
-    - picard
   files:
     - path: output/picard/test.marked.MarkDuplicates.metrics.txt
       contains:
         - "1.0	0.999986	1178"
-    - path: ./output/picard/test.marked.bam
-- name: picard markduplicates sorted cram stub
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config -stub-run
-  tags:
-    - picard/markduplicates
-    - picard
-  files:
-    - path: output/picard/test.marked.MarkDuplicates.metrics.txt
-    - path: ./output/picard/test.marked.bam
+    - path: output/picard/test.marked.bam
+      md5sum: 80eb6c43eb6982ee55bb06f59001cbe6
+    - path: output/picard/versions.yml