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test: new tests for picard/samtofastq
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process { | ||
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
withName: "test_picard_samtofastq_paired_keep_unpaired" { | ||
ext.args = "--UNPAIRED_FASTQ test.unpaired.fastq" | ||
} | ||
} |
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- name: picard samtofastq test_picard_samtofastq_single | ||
command: nextflow run ./tests/modules/CCBR/picard/samtofastq -entry test_picard_samtofastq_single -c ./tests/config/nextflow.config | ||
tags: | ||
- picard/samtofastq | ||
- picard | ||
files: | ||
- path: output/picard/test.fastq.gz | ||
contains: | ||
- "@ERR5069949.2151832" | ||
- path: output/picard/versions.yml | ||
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- name: picard samtofastq test_picard_samtofastq_paired | ||
command: nextflow run ./tests/modules/CCBR/picard/samtofastq -entry test_picard_samtofastq_paired -c ./tests/config/nextflow.config | ||
tags: | ||
- picard/samtofastq | ||
- picard | ||
files: | ||
- path: output/picard/test_1.fastq.gz | ||
contains: | ||
- "@ERR5069949.2151832/1" | ||
- path: output/picard/test_2.fastq.gz | ||
contains: | ||
- "@ERR5069949.2151832/2" | ||
- path: output/picard/test.unpaired.fastq.gz | ||
- path: output/picard/versions.yml | ||
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- name: picard samtofastq test_picard_samtofastq_single stub | ||
command: nextflow run ./tests/modules/CCBR/picard/samtofastq -entry test_picard_samtofastq_single -c ./tests/config/nextflow.config -stub | ||
tags: | ||
- picard/samtofastq | ||
- picard | ||
files: | ||
- path: output/picard/test.fastq.gz | ||
- path: output/picard/versions.yml |