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fix more ver yml (#757)

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* Fix featurecounts

* whitespace change to trigger CI on yara/mapper

* update test yaml
This commit is contained in:
Gregor Sturm 2021-09-28 21:25:10 +02:00 committed by GitHub
parent cde1d827f9
commit c3687ef54b
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 12 additions and 12 deletions
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2
modules/subread/featurecounts/main.nf
View file

@ -49,7 +49,7 @@ process SUBREAD_FEATURECOUNTS {
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}: ${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(featureCounts -v 2>&1 | sed -e "s/featureCounts v//g") ${getSoftwareName(task.process)}: \$( echo \$(featureCounts -v 2>&1) | sed -e "s/featureCounts v//g")
END_VERSIONS END_VERSIONS
""" """
} }

18
tests/modules/subread/featurecounts/test.yml
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@ -4,10 +4,10 @@
- subread - subread
- subread/featurecounts - subread/featurecounts
files: files:
- path: output/subread/test.featureCounts.txt.summary
md5sum: d78617192451a57f6ef249ddcaf13720
- path: output/subread/test.featureCounts.txt - path: output/subread/test.featureCounts.txt
md5sum: b0a1f7563afe49007f422d4c9ca5ee6c md5sum: 0012df4c0a0e47eec1440017ab34f75f
- path: output/subread/test.featureCounts.txt.summary
md5sum: 8f602ff9a8ef467af43294e80b367cdf
- name: subread featurecounts test_subread_featurecounts_reverse - name: subread featurecounts test_subread_featurecounts_reverse
command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config
@ -15,10 +15,10 @@
- subread - subread
- subread/featurecounts - subread/featurecounts
files: files:
- path: output/subread/test.featureCounts.txt.summary
md5sum: 4217004d0b55f870f77092364f59e44d
- path: output/subread/test.featureCounts.txt - path: output/subread/test.featureCounts.txt
md5sum: 412840a8880cd29674b3d5404d3de19b md5sum: 8175816b8260ed444d59232bd7e7120b
- path: output/subread/test.featureCounts.txt.summary
md5sum: 7cfa30ad678b9bc1bc63afbb0281547b
- name: subread featurecounts test_subread_featurecounts_unstranded - name: subread featurecounts test_subread_featurecounts_unstranded
command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config
@ -26,7 +26,7 @@
- subread - subread
- subread/featurecounts - subread/featurecounts
files: files:
- path: output/subread/test.featureCounts.txt.summary
md5sum: ee585faeb1edfcd2188a5e486a0e98a9
- path: output/subread/test.featureCounts.txt - path: output/subread/test.featureCounts.txt
md5sum: 6b684e11a1e54bec7e1ee5e3f651d7fd md5sum: 3307d31b44a5d6bb3389786bb8f4e91f
- path: output/subread/test.featureCounts.txt.summary
md5sum: 23164b79f9f23f11c82820db61a35560

4
tests/modules/yara/mapper/main.nf
View file

@ -3,8 +3,8 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams( options: ['args': '-e 3'] ) include { YARA_INDEX } from '../../../../modules/yara/index/main.nf' addParams(options: ['args': '-e 3'])
include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf' addParams( options: ['args': '-e 3'] ) include { YARA_MAPPER } from '../../../../modules/yara/mapper/main.nf' addParams(options: ['args': '-e 3'])
workflow test_yara_single_end { workflow test_yara_single_end {