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Merge remote-tracking branch 'origin' into gatk_spark

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SusiJo 2022-06-07 14:00:26 +02:00
commit e78ad2f88b
2 changed files with 8 additions and 7 deletions
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3
modules/gatk4/calibratedragstrmodel/main.nf
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@ -1,6 +1,6 @@
process GATK4_CALIBRATEDRAGSTRMODEL { process GATK4_CALIBRATEDRAGSTRMODEL {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@ -38,6 +38,7 @@ process GATK4_CALIBRATEDRAGSTRMODEL {
--output ${prefix}.txt \\ --output ${prefix}.txt \\
--reference $fasta \\ --reference $fasta \\
--str-table-path $strtablefile \\ --str-table-path $strtablefile \\
--threads $task.cpus \\
$intervals_command \\ $intervals_command \\
--tmp-dir . \\ --tmp-dir . \\
$args $args

12
tests/modules/gatk4/calibratedragstrmodel/test.yml
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@ -1,26 +1,26 @@
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_bam - 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 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: tags:
- gatk4/calibratedragstrmodel
- gatk4 - gatk4
- gatk4/calibratedragstrmodel
files: files:
- path: output/gatk4/test.txt - path: output/gatk4/test.txt
md5sum: 0a1a1583b157fa2251dd931ed165da4f md5sum: e16fa32906c74bb18b93e98a86718ff1
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_cram - 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 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: tags:
- gatk4/calibratedragstrmodel
- gatk4 - gatk4
- gatk4/calibratedragstrmodel
files: files:
- path: output/gatk4/test.txt - path: output/gatk4/test.txt
md5sum: 1aa7ab38023f724877b3323c5e6b9a4e md5sum: 81c7bf338886cb4d5c2cc07fc56afe44
- name: gatk4 calibratedragstrmodel test_gatk4_calibratedragstrmodel_beds - 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 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: tags:
- gatk4/calibratedragstrmodel
- gatk4 - gatk4
- gatk4/calibratedragstrmodel
files: files:
- path: output/gatk4/test.txt - path: output/gatk4/test.txt
md5sum: def8baccad7bd59006f08fcb0a6721bf md5sum: cb6a9acdee042302b54fd1f59b5f54ee