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Revert since fixes to test were not working

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This reverts commit d7a219e88d.
This commit is contained in:
JoseEspinosa 2021-02-12 18:02:32 +01:00
parent 8e23e1839d
commit 0688230863
2 changed files with 6 additions and 6 deletions
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4
software/cat/fastq/main.nf
View file

@ -1,5 +1,5 @@
// Import generic module functions // Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles } from './functions'
params.options = [:] params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
@ -8,7 +8,7 @@ process CAT_FASTQ {
tag "$meta.id" tag "$meta.id"
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', publish_id:meta.id) }
conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null) conda (params.enable_conda ? "conda-forge::sed=4.7=h1bed415_1000" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

8
tests/software/cat/fastq/test.yml
View file

@ -5,17 +5,17 @@
- fastq - fastq
- cat_fastqc_single_end - cat_fastqc_single_end
files: files:
- path: output/cat/test.merged.fastq.gz - path: output/merged_fastq/test.merged.fastq.gz
md5sum: 7f753b793e5b0872758b1574db84d767 md5sum: 7f753b793e5b0872758b1574db84d767
- name: cat fastq paired-end - name: cat fastq fastqc_paired_end
command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_paired_end -c tests/config/nextflow.config
tags: tags:
- cat - cat
- fastq - fastq
- cat_fastqc_paired_end - cat_fastqc_paired_end
files: files:
- path: output/cat/test_1.merged.fastq.gz - path: output/merged_fastq/test_1.merged.fastq.gz
md5sum: 7f753b793e5b0872758b1574db84d767 md5sum: 7f753b793e5b0872758b1574db84d767
- path: output/cat/test_2.merged.fastq.gz - path: output/merged_fastq/test_2.merged.fastq.gz
md5sum: c71ff917e002b1e852916a021d52921d md5sum: c71ff917e002b1e852916a021d52921d