diff --git a/modules/subread/featurecounts/main.nf b/modules/subread/featurecounts/main.nf index 3e2eb765..76209a0d 100644 --- a/modules/subread/featurecounts/main.nf +++ b/modules/subread/featurecounts/main.nf @@ -49,7 +49,7 @@ process SUBREAD_FEATURECOUNTS { cat <<-END_VERSIONS > versions.yml ${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 """ } diff --git a/tests/modules/subread/featurecounts/test.yml b/tests/modules/subread/featurecounts/test.yml index 2cba9e15..be6bed47 100644 --- a/tests/modules/subread/featurecounts/test.yml +++ b/tests/modules/subread/featurecounts/test.yml @@ -4,10 +4,10 @@ - subread - subread/featurecounts files: - - path: output/subread/test.featureCounts.txt.summary - md5sum: d78617192451a57f6ef249ddcaf13720 - 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 command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_reverse -c tests/config/nextflow.config @@ -15,10 +15,10 @@ - subread - subread/featurecounts files: - - path: output/subread/test.featureCounts.txt.summary - md5sum: 4217004d0b55f870f77092364f59e44d - 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 command: nextflow run tests/modules/subread/featurecounts -entry test_subread_featurecounts_unstranded -c tests/config/nextflow.config @@ -26,7 +26,7 @@ - subread - subread/featurecounts files: - - path: output/subread/test.featureCounts.txt.summary - md5sum: ee585faeb1edfcd2188a5e486a0e98a9 - path: output/subread/test.featureCounts.txt - md5sum: 6b684e11a1e54bec7e1ee5e3f651d7fd + md5sum: 3307d31b44a5d6bb3389786bb8f4e91f + - path: output/subread/test.featureCounts.txt.summary + md5sum: 23164b79f9f23f11c82820db61a35560 diff --git a/tests/modules/yara/mapper/main.nf b/tests/modules/yara/mapper/main.nf index 06582eb3..9cdce40d 100644 --- a/tests/modules/yara/mapper/main.nf +++ b/tests/modules/yara/mapper/main.nf @@ -3,8 +3,8 @@ nextflow.enable.dsl = 2 -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_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']) workflow test_yara_single_end {