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adjusted prefix + test + authors

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This commit is contained in:
SusiJo 2022-06-07 13:58:57 +02:00
parent 1368956d88
commit dbca9e8b36
4 changed files with 12 additions and 2 deletions
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2
modules/gatk4/markduplicatesspark/main.nf
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@ -23,7 +23,7 @@ process GATK4_MARKDUPLICATES_SPARK {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" prefix = task.ext.prefix ?: "${meta.id}"
def input_list = bam.collect{"--input $it"}.join(' ') def input_list = bam.collect{"--input $it"}.join(' ')

1
modules/gatk4/markduplicatesspark/meta.yml
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@ -58,3 +58,4 @@ authors:
- "@ajodeh-juma" - "@ajodeh-juma"
- "@FriederikeHanssen" - "@FriederikeHanssen"
- "@maxulysse" - "@maxulysse"
- "@SusiJo"

2
tests/modules/gatk4/markduplicatesspark/nextflow.config
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@ -9,8 +9,8 @@ process {
ext.prefix = { "${meta.id}.cram" } ext.prefix = { "${meta.id}.cram" }
} }
withName: GATK4_MARKDUPLICATES_SPARK_METRICS { withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
ext.prefix = { "${meta.id}.bam" }
ext.args = '--metrics-file test.metrics' ext.args = '--metrics-file test.metrics'
ext.prefix = { "${meta.id}.bam" }
} }
} }

9
tests/modules/gatk4/markduplicatesspark/test.yml
View file

@ -16,6 +16,15 @@
- path: output/gatk4/test.bam - path: output/gatk4/test.bam
md5sum: 898cb0a6616897d8ada90bab53bf0837 md5sum: 898cb0a6616897d8ada90bab53bf0837
- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_cram_out
command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_cram_out -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
tags:
- gatk4
- gatk4/markduplicatesspark
files:
- path: output/gatk4/test.cram
md5sum: 2271016de5e4199736598f39d12d7587
- name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_metrics - name: gatk4 markduplicatesspark test_gatk4_markduplicates_spark_multiple_bams_metrics
command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_metrics -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config command: nextflow run ./tests/modules/gatk4/markduplicatesspark -entry test_gatk4_markduplicates_spark_multiple_bams_metrics -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicatesspark/nextflow.config
tags: tags: