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Faqcs patch to add tests for --debug output (#1368)

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* faqcs update to capture debug output

* change paths

* change nf.config on faqcs

* Updated test,yml on faqcs

Co-authored-by: Cipriano <rrn8@cdc.gov>
This commit is contained in:
Michael J Cipriano 2022-03-02 08:53:05 -05:00 committed by GitHub
parent 2cd502a236
commit fba1b381f5
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2 changed files with 25 additions and 0 deletions
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1
tests/modules/faqcs/nextflow.config
View file

@ -1,5 +1,6 @@
process { process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.args = {"--debug" }
} }

24
tests/modules/faqcs/test.yml
View file

@ -3,8 +3,20 @@
tags: tags:
- faqcs - faqcs
files: files:
- path: output/faqcs/qa.test.base_content.txt
md5sum: f992603f01ca430c03c8aae02eba2f5d
- path: output/faqcs/qa.test.for_qual_histogram.txt
md5sum: a3d462ab84151e982f99f85f52c21de3
- path: output/faqcs/qa.test.length_count.txt
md5sum: 80915f09fbaf5884c32e95acab2d031c
- path: output/faqcs/test.base_content.txt
md5sum: f992603f01ca430c03c8aae02eba2f5d
- path: output/faqcs/test.fastp.log - path: output/faqcs/test.fastp.log
md5sum: be79dc893f87de1f82faf749cdfb848c md5sum: be79dc893f87de1f82faf749cdfb848c
- path: output/faqcs/test.for_qual_histogram.txt
md5sum: a3d462ab84151e982f99f85f52c21de3
- path: output/faqcs/test.length_count.txt
md5sum: 80915f09fbaf5884c32e95acab2d031c
- path: output/faqcs/test.stats.txt - path: output/faqcs/test.stats.txt
md5sum: ea20e93706b2e4c676004253baa3cec6 md5sum: ea20e93706b2e4c676004253baa3cec6
- path: output/faqcs/test.trimmed.fastq.gz - path: output/faqcs/test.trimmed.fastq.gz
@ -18,8 +30,20 @@
tags: tags:
- faqcs - faqcs
files: files:
- path: output/faqcs/qa.test.base_content.txt
md5sum: 99aa9a775ccd8d6503f0cf80f775203c
- path: output/faqcs/qa.test.for_qual_histogram.txt
md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
- path: output/faqcs/qa.test.length_count.txt
md5sum: 420298983c762754d5b0ef32c9d5dad4
- path: output/faqcs/test.base_content.txt
md5sum: 99aa9a775ccd8d6503f0cf80f775203c
- path: output/faqcs/test.fastp.log - path: output/faqcs/test.fastp.log
md5sum: be79dc893f87de1f82faf749cdfb848c md5sum: be79dc893f87de1f82faf749cdfb848c
- path: output/faqcs/test.for_qual_histogram.txt
md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
- path: output/faqcs/test.length_count.txt
md5sum: 420298983c762754d5b0ef32c9d5dad4
- path: output/faqcs/test.stats.txt - path: output/faqcs/test.stats.txt
md5sum: 9a693f8af94ab8c485519d9a523aa622 md5sum: 9a693f8af94ab8c485519d9a523aa622
- path: output/faqcs/test_1.trimmed.fastq.gz - path: output/faqcs/test_1.trimmed.fastq.gz