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Code Issues Releases Packages Activity

few version and test data config fixes (#758)

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* update kleborate version info

* fix stderr capture

* few more version fixes

* fix version info on more tools
This commit is contained in:
Robert A. Petit III 2021-09-28 13:42:04 -06:00 committed by GitHub
parent c3687ef54b
commit 5c463ca6b4
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GPG key ID: 4AEE18F83AFDEB23
12 changed files with 21 additions and 20 deletions
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13
modules/chromap/chromap/main.nf
View file

@ -41,9 +41,7 @@ process CHROMAP_CHROMAP {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def args = options.args.tokenize()
def file_extension = options.args.contains("--SAM")? 'sam' :
options.args.contains("--TagAlign")? 'tagAlign' :
options.args.contains("--pairs")? 'pairs' : 'bed'
def file_extension = options.args.contains("--SAM") ? 'sam' : options.args.contains("--TagAlign")? 'tagAlign' : options.args.contains("--pairs")? 'pairs' : 'bed'
if (barcodes) {
args << "-b ${barcodes.join(',')}"
if (whitelist) {
@ -56,9 +54,8 @@ process CHROMAP_CHROMAP {
if (pairs_chr_order){
args << "--pairs-natural-chr-order $pairs_chr_order"
}
def compression_cmds = """
gzip ${prefix}.${file_extension}
"""
def final_args = args.join(' ')
def compression_cmds = "gzip ${prefix}.${file_extension}"
if (options.args.contains("--SAM")) {
compression_cmds = """
samtools view $options.args2 -@ ${task.cpus} -bh \\
@ -68,7 +65,7 @@ process CHROMAP_CHROMAP {
}
if (meta.single_end) {
"""
chromap ${args.join(' ')} \\
chromap ${final_args} \\
-t $task.cpus \\
-x $index \\
-r $fasta \\
@ -84,7 +81,7 @@ process CHROMAP_CHROMAP {
"""
} else {
"""
chromap ${args.join(' ')} \\
chromap ${final_args} \\
-t $task.cpus \\
-x $index \\
-r $fasta \\

2
modules/delly/call/main.nf
View file

@ -41,7 +41,7 @@ process DELLY_CALL {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(delly --version 2>&1 | sed 's/^.*Delly //; s/Using.*\$//')
${getSoftwareName(task.process)}: \$( echo \$(delly --version 2>&1) | sed 's/^.*Delly version: v//; s/ using.*\$//')
END_VERSIONS
"""
}

2
modules/ensemblvep/main.nf
View file

@ -59,7 +59,7 @@ process ENSEMBLVEP {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(vep --help 2>&1)
${getSoftwareName(task.process)}: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
END_VERSIONS
"""
}

2
modules/expansionhunter/main.nf
View file

@ -42,7 +42,7 @@ process EXPANSIONHUNTER {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(ExpansionHunter --version 2>&1 | sed 's/^.*ExpansionHunter //')
${getSoftwareName(task.process)}: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
END_VERSIONS
"""
}

3
modules/fgbio/callmolecularconsensusreads/main.nf
View file

@ -33,9 +33,10 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
-i $bam \\
$options.args \\
-o ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(fgbio --version | sed -e "s/fgbio v//g")
${getSoftwareName(task.process)}: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
END_VERSIONS
"""
}

2
modules/fgbio/sortbam/main.nf
View file

@ -35,7 +35,7 @@ process FGBIO_SORTBAM {
-o ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(fgbio --version | sed -e "s/fgbio v//g")
${getSoftwareName(task.process)}: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
END_VERSIONS
"""
}

3
modules/glnexus/main.nf
View file

@ -44,9 +44,10 @@ process GLNEXUS {
$options.args \\
${input.join(' ')} \\
> ${prefix}.bcf
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(glnexus_cli 2>&1 | head -n 1 | sed 's/^.*release //; s/ .*\$//')
${getSoftwareName(task.process)}: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
END_VERSIONS
"""
}

2
modules/kleborate/main.nf
View file

@ -36,7 +36,7 @@ process KLEBORATE {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(kleborate -v 2>&1 | sed 's/kleborate //;')
${getSoftwareName(task.process)}: \$( echo \$(kleborate --version | sed 's/Kleborate v//;'))
END_VERSIONS
"""
}

5
modules/minia/main.nf
View file

@ -30,8 +30,9 @@ process MINIA {
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def read_list = reads.join(",")
"""
echo "${reads.join("\n")}" > input_files.txt
echo "${read_list}" | sed 's/,/\\n/g' > input_files.txt
minia \\
$options.args \\
-nb-cores $task.cpus \\
@ -40,7 +41,7 @@ process MINIA {
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(minia --version 2>&1) | sed 's/^.*Minia version //; s/ .*\$//')
${getSoftwareName(task.process)}: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
END_VERSIONS
"""
}

1
tests/config/test_data.config
View file

@ -180,6 +180,7 @@ params {
ccs_fq = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
ccs_fq_gz = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
ccs_xml = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
hifi = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
lima = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
refine = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
cluster = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"

2
tests/modules/delly/call/test.yml
View file

@ -5,6 +5,6 @@
- delly/call
files:
- path: output/delly/test.bcf
md5sum: b20df3b9086faccd6bfd2641d97712c8
md5sum: 360c1bf6867f33bd2a868ddfb4d957fc
- path: output/delly/test.bcf.csi
md5sum: 19e0cdf06c415f4942f6d4dbd5fb7271

4
tests/modules/hifiasm/main.nf
View file

@ -10,7 +10,7 @@ include { HIFIASM } from '../../../modules/hifiasm/main.nf' addParams( options:
workflow test_hifiasm_hifi_only {
input = [
[ id:'test' ], // meta map
[ file(params.test_data['homo_sapiens']['pacbio']['test_hifi_fastq_gz'], checkIfExists: true) ]
[ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
]
HIFIASM ( input, [], [], false )
@ -22,7 +22,7 @@ workflow test_hifiasm_hifi_only {
workflow test_hifiasm_with_parental_reads {
input = [
[ id:'test' ], // meta map
[ file(params.test_data['homo_sapiens']['pacbio']['test_hifi_fastq_gz'], checkIfExists: true) ]
[ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ]
]
paternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test_yak'], checkIfExists: true)
maternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test2_yak'], checkIfExists: true)