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Fix yml ver (#756)
* Fix kallisto index tests * Fix nanoplot * Fix kallistobustools * Fix pairix * Fix plasmidid * Fix pbccs * Fix raxmlng * Fix prokka * Fix shovill * Fix typo * Deleted workflow by mistake added again
This commit is contained in:
Jose Espinosa-Carrasco
GitHub
parent
512f5dfc27
commit
cde1d827f9
13 changed files with 14 additions and 15 deletions
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@ -36,7 +36,7 @@ process KALLISTO_INDEX {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(kallisto 2>&1 | sed 's/^kallisto //; s/Usage.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//')
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END_VERSIONS
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"""
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}
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@ -1,7 +1,7 @@
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name: kallisto_index
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description: write your description here
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description: Create kallisto index
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keywords:
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- sort
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- index
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tools:
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- kallisto:
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description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
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@ -53,7 +53,7 @@ process KALLISTOBUSTOOLS_COUNT {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
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END_VERSIONS
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"""
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}
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@ -47,7 +47,7 @@ process KALLISTOBUSTOOLS_REF {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
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END_VERSIONS
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"""
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} else {
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@ -66,7 +66,7 @@ process KALLISTOBUSTOOLS_REF {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(kb 2>&1 | sed 's/^.*kb_python //;s/positional arguments.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
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END_VERSIONS
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"""
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}
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@ -39,7 +39,7 @@ process NANOPLOT {
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$input_file
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(NanoPlot --version 2>&1 | sed 's/^.*NanoPlot //; s/ .*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -34,7 +34,7 @@ process PAIRIX {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(pairix --help 2>&1 | sed 's/^.*Version: //; s/Usage.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
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END_VERSIONS
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"""
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}
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@ -51,7 +51,7 @@ process PBCCS {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(ccs --version 2>&1 | grep -e 'commit')
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${getSoftwareName(task.process)}: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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@ -47,7 +47,7 @@ process PLASMIDID {
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mv NO_GROUP/$prefix ./$prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(plasmidID --version 2>&1)
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${getSoftwareName(task.process)}: \$(echo \$(plasmidID --version 2>&1))
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END_VERSIONS
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"""
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}
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@ -36,7 +36,7 @@ process RAXMLNG {
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(raxml-ng --version 2>&1 | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
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${getSoftwareName(task.process)}: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
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END_VERSIONS
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"""
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}
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@ -7,7 +7,7 @@ include { KALLISTO_INDEX } from '../../../../modules/kallisto/index/main.nf' add
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workflow test_kallisto_index {
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def input = []
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input = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
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input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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KALLISTO_INDEX ( input )
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}
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@ -2,7 +2,7 @@
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nextflow.enable.dsl = 2
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include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger"] )
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include { KALLISTOBUSTOOLS_COUNT } from '../../../../modules/kallistobustools/count/main.nf' addParams( options: [args:"--cellranger -m 1"] )
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workflow test_kallistobustools_count {
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@ -30,3 +30,4 @@ workflow test_kallistobustools_ref_nucleus {
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KALLISTOBUSTOOLS_REF( fasta, gtf, workflow)
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}
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@ -12,7 +12,6 @@
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- path: output/plasmidid/test/data/test.fna
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md5sum: 503a5e1d4654bb2df19420e211070db3
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- path: output/plasmidid/test/data/test.gbk
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md5sum: c851bba9da6ec72cce591617067df50b
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- path: output/plasmidid/test/data/test.gff
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md5sum: 3ed8912ee9b0712ca491fa78ff5f4da1
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- path: output/plasmidid/test/data/test.karyotype_individual.txt
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@ -28,7 +27,6 @@
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- path: output/plasmidid/test/database/test.fna
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md5sum: 6b843fe652b4369addb382f61952c3dd
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- path: output/plasmidid/test/database/test.gbk
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md5sum: 1f7972ecbb868823727157d2c482700d
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- path: output/plasmidid/test/database/test.gff
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md5sum: 7e65da147d0a413020b0d92b7b03ffcd
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- path: output/plasmidid/test/fasta_files/MT192765.1_term.fasta
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