FIX: More coherence in all gatk4spark modules (nf-core#4282)

* fix gatk4 version * rename and update all gatk4_<module>spark to gatk4spark_<module> * update pytest_modules.yml * fix meta.yml * fix typo * remove now useless exclude statements * fix output path
maxulysse · Nov 2, 2023 · c3aaaa6 · c3aaaa6
1 parent bdbbd9a
commit c3aaaa6
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Showing 25 changed files with 273 additions and 277 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -223,16 +223,12 @@ jobs:
             tags: fcs/fcsadaptor
           - profile: "conda"
             tags: fcs/fcsgx
-          - profile: "conda"
-            tags: gatk4/baserecalibratorspark
           - profile: "conda"
             tags: gatk4/cnnscorevariants
           - profile: "conda"
             tags: gatk4/determinegermlinecontigploidy
           - profile: "conda"
             tags: gatk4/germlinecnvcaller
-          - profile: "conda"
-            tags: gatk4/markduplicatesspark
           - profile: "conda"
             tags: gatk4/postprocessgermlinecnvcalls
           - profile: "conda"

diff --git a/...core/gatk4/applybqsrspark/environment.yml → ...core/gatk4spark/applybqsr/environment.yml b/...core/gatk4/applybqsrspark/environment.yml → ...core/gatk4spark/applybqsr/environment.yml
@@ -3,5 +3,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.3.0.0
-  - conda-forge::openjdk=8.0.312
+  - bioconda::gatk4-spark=4.4.0.0
diff --git a/modules/nf-core/gatk4/applybqsrspark/main.nf → modules/nf-core/gatk4spark/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf → modules/nf-core/gatk4spark/applybqsr/main.nf
@@ -1,9 +1,11 @@
-process GATK4_APPLYBQSR_SPARK {
+process GATK4SPARK_APPLYBQSR {
     tag "$meta.id"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "nf-core/gatk:4.4.0.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0':
+        'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

diff --git a/...les/nf-core/gatk4/applybqsrspark/meta.yml → ...les/nf-core/gatk4spark/applybqsr/meta.yml b/...les/nf-core/gatk4/applybqsrspark/meta.yml → ...les/nf-core/gatk4spark/applybqsr/meta.yml
@@ -1,12 +1,11 @@
-name: gatk4_applybqsr_spark
+name: gatk4spark_applybqsr
 description: Apply base quality score recalibration (BQSR) to a bam file
 keywords:
   - bam
   - base quality score recalibration
   - bqsr
   - cram
-  - gatk4
-  - spark
+  - gatk4spark
 tools:
   - gatk4:
       description: |

diff --git a/...gatk4/markduplicatesspark/environment.yml → ...tk4spark/baserecalibrator/environment.yml b/...gatk4/markduplicatesspark/environment.yml → ...tk4spark/baserecalibrator/environment.yml
@@ -3,5 +3,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
-  - conda-forge::openjdk=8.0.312
+  - bioconda::gatk4-spark=4.4.0.0
diff --git a/...-core/gatk4/baserecalibratorspark/main.nf → ...-core/gatk4spark/baserecalibrator/main.nf b/...-core/gatk4/baserecalibratorspark/main.nf → ...-core/gatk4spark/baserecalibrator/main.nf
@@ -1,9 +1,11 @@
-process GATK4_BASERECALIBRATOR_SPARK {
+process GATK4SPARK_BASERECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "nf-core/gatk:4.4.0.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0':
+        'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

diff --git a/...core/gatk4/baserecalibratorspark/meta.yml → ...core/gatk4spark/baserecalibrator/meta.yml b/...core/gatk4/baserecalibratorspark/meta.yml → ...core/gatk4spark/baserecalibrator/meta.yml
@@ -1,12 +1,11 @@
-name: gatk4_baserecalibrator_spark
+name: gatk4spark_baserecalibrator
 description: Generate recalibration table for Base Quality Score Recalibration (BQSR)
 keywords:
   - base quality score recalibration
   - table
   - bqsr
-  - gatk4
+  - gatk4spark
   - sort
-  - spark
 tools:
   - gatk4:
       description: |

diff --git a/...tk4/baserecalibratorspark/environment.yml → ...gatk4spark/markduplicates/environment.yml b/...tk4/baserecalibratorspark/environment.yml → ...gatk4spark/markduplicates/environment.yml
@@ -3,5 +3,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gatk4=4.4.0.0
-  - conda-forge::openjdk=8.0.312
+  - bioconda::gatk4-spark=4.4.0.0
diff --git a/...nf-core/gatk4/markduplicatesspark/main.nf → ...nf-core/gatk4spark/markduplicates/main.nf b/...nf-core/gatk4/markduplicatesspark/main.nf → ...nf-core/gatk4spark/markduplicates/main.nf
@@ -1,9 +1,11 @@
-process GATK4_MARKDUPLICATES_SPARK {
+process GATK4SPARK_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "nf-core/gatk:4.4.0.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4-spark:4.4.0.0--hdfd78af_0':
+        'biocontainers/gatk4-spark:4.4.0.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

diff --git a/...f-core/gatk4/markduplicatesspark/meta.yml → ...f-core/gatk4spark/markduplicates/meta.yml b/...f-core/gatk4/markduplicatesspark/meta.yml → ...f-core/gatk4spark/markduplicates/meta.yml
@@ -1,11 +1,10 @@
-name: gatk4_markduplicates_spark
+name: gatk4spark_markduplicates
 description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
 keywords:
   - bam
-  - gatk4
+  - gatk4spark
   - markduplicates
   - sort
-  - spark
 tools:
   - gatk4:
       description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1237,10 +1237,6 @@ gatk4/applybqsr:
   - modules/nf-core/gatk4/applybqsr/**
   - tests/modules/nf-core/gatk4/applybqsr/**
 
-gatk4/applybqsrspark:
-  - modules/nf-core/gatk4/applybqsrspark/**
-  - tests/modules/nf-core/gatk4/applybqsrspark/**
-
 gatk4/applyvqsr:
   - modules/nf-core/gatk4/applyvqsr/**
   - tests/modules/nf-core/gatk4/applyvqsr/**
@@ -1253,10 +1249,6 @@ gatk4/baserecalibrator:
   - modules/nf-core/gatk4/baserecalibrator/**
   - tests/modules/nf-core/gatk4/baserecalibrator/**
 
-gatk4/baserecalibratorspark:
-  - modules/nf-core/gatk4/baserecalibratorspark/**
-  - tests/modules/nf-core/gatk4/baserecalibratorspark/**
-
 gatk4/bedtointervallist:
   - modules/nf-core/gatk4/bedtointervallist/**
   - tests/modules/nf-core/gatk4/bedtointervallist/**
@@ -1385,10 +1377,6 @@ gatk4/markduplicates:
   - modules/nf-core/gatk4/markduplicates/**
   - tests/modules/nf-core/gatk4/markduplicates/**
 
-gatk4/markduplicatesspark:
-  - modules/nf-core/gatk4/markduplicatesspark/**
-  - tests/modules/nf-core/gatk4/markduplicatesspark/**
-
 gatk4/mergebamalignment:
   - modules/nf-core/gatk4/mergebamalignment/**
   - tests/modules/nf-core/gatk4/mergebamalignment/**
@@ -1477,6 +1465,18 @@ gatk4/variantrecalibrator:
   - modules/nf-core/gatk4/variantrecalibrator/**
   - tests/modules/nf-core/gatk4/variantrecalibrator/**
 
+gatk4spark/applybqsr:
+  - modules/nf-core/gatk4spark/applybqsr/**
+  - tests/modules/nf-core/gatk4spark/applybqsr/**
+
+gatk4spark/baserecalibrator:
+  - modules/nf-core/gatk4spark/baserecalibrator/**
+  - tests/modules/nf-core/gatk4spark/baserecalibrator/**
+
+gatk4spark/markduplicates:
+  - modules/nf-core/gatk4spark/markduplicates/**
+  - tests/modules/nf-core/gatk4spark/markduplicates/**
+
 gawk:
   - modules/nf-core/gawk/**
   - tests/modules/nf-core/gawk/**

diff --git a/tests/modules/nf-core/gatk4/applybqsrspark/main.nf b/tests/modules/nf-core/gatk4/applybqsrspark/main.nf
diff --git a/tests/modules/nf-core/gatk4/applybqsrspark/test.yml b/tests/modules/nf-core/gatk4/applybqsrspark/test.yml
diff --git a/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf b/tests/modules/nf-core/gatk4/baserecalibratorspark/main.nf
diff --git a/tests/modules/nf-core/gatk4/baserecalibratorspark/test.yml b/tests/modules/nf-core/gatk4/baserecalibratorspark/test.yml