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Patch getsoftwareversions java tools #890

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Merged
jfy133 merged 4 commits into from
Jul 4, 2022
Merged

Patch getsoftwareversions java tools #890

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4d7e1c0
Add memory to all java tools in get_software_versions
jfy133 May 30, 2022
1dcd882
Phrasing Tweak
jfy133 May 30, 2022
ebba956
Fix issue number in link
jfy133 May 30, 2022
b974bf1
Relace bbduk version with bbversion.sh
jfy133 Jun 3, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
- [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
- [#885](https://github.com/nf-core/eager/issues/885) Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)

### `Dependencies`

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28 changes: 14 additions & 14 deletions main.nf
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Expand Up @@ -3113,39 +3113,39 @@ process get_software_versions {
echo $workflow.manifest.version &> v_pipeline.txt
echo $workflow.nextflow.version &> v_nextflow.txt

fastqc --version &> v_fastqc.txt 2>&1 || true
fastqc -t ${task.cpus} --version &> v_fastqc.txt 2>&1 || true
AdapterRemoval --version &> v_adapterremoval.txt 2>&1 || true
fastp --version &> v_fastp.txt 2>&1 || true
bwa &> v_bwa.txt 2>&1 || true
circulargenerator --help | head -n 1 &> v_circulargenerator.txt 2>&1 || true
circulargenerator -Xmx${task.memory.toGiga()}g --help | head -n 1 &> v_circulargenerator.txt 2>&1 || true
samtools --version &> v_samtools.txt 2>&1 || true
dedup -v &> v_dedup.txt 2>&1 || true
dedup -Xmx${task.memory.toGiga()}g -v &> v_dedup.txt 2>&1 || true
## bioconda recipe of picard is incorrectly set up and extra warning made with stderr, this ugly command ensures only version exported
( exec 7>&1; picard MarkDuplicates --version 2>&1 >&7 | grep -v '/' >&2 ) 2> v_markduplicates.txt || true
qualimap --version &> v_qualimap.txt 2>&1 || true
( exec 7>&1; picard -Xmx${task.memory.toMega()}M MarkDuplicates --version 2>&1 >&7 | grep -v '/' >&2 ) 2> v_markduplicates.txt || true
qualimap --version --java-mem-size=${task.memory.toGiga()}G &> v_qualimap.txt 2>&1 || true
preseq &> v_preseq.txt 2>&1 || true
gatk --version 2>&1 | grep '(GATK)' > v_gatk.txt 2>&1 || true
gatk3 --version 2>&1 | head -n 1 > v_gatk3.txt 2>&1 || true
gatk --java-options "-Xmx${task.memory.toGiga()}G" --version 2>&1 | grep '(GATK)' > v_gatk.txt 2>&1 || true
gatk3 -Xmx${task.memory.toGiga()}g --version 2>&1 | head -n 1 > v_gatk3.txt 2>&1 || true
freebayes --version &> v_freebayes.txt 2>&1 || true
bedtools --version &> v_bedtools.txt 2>&1 || true
damageprofiler --version &> v_damageprofiler.txt 2>&1 || true
damageprofiler -Xmx${task.memory.toGiga()}g --version &> v_damageprofiler.txt 2>&1 || true
bam --version &> v_bamutil.txt 2>&1 || true
pmdtools --version &> v_pmdtools.txt 2>&1 || true
angsd -h |& head -n 1 | cut -d ' ' -f3-4 &> v_angsd.txt 2>&1 || true
multivcfanalyzer --help | head -n 1 &> v_multivcfanalyzer.txt 2>&1 || true
malt-run --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' &> v_malt.txt 2>&1 || true
MaltExtract --help | head -n 2 | tail -n 1 &> v_maltextract.txt 2>&1 || true
multivcfanalyzer -Xmx${task.memory.toGiga()}g --help | head -n 1 &> v_multivcfanalyzer.txt 2>&1 || true
malt-run -J-Xmx${task.memory.toGiga()}g --help |& tail -n 3 | head -n 1 | cut -f 2 -d'(' | cut -f 1 -d ',' &> v_malt.txt 2>&1 || true
MaltExtract -Xmx${task.memory.toGiga()}g --help | head -n 2 | tail -n 1 &> v_maltextract.txt 2>&1 || true
multiqc --version &> v_multiqc.txt 2>&1 || true
vcf2genome -h |& head -n 1 &> v_vcf2genome.txt || true
mtnucratio --help &> v_mtnucratiocalculator.txt || true
vcf2genome -Xmx${task.memory.toGiga()}g -h |& head -n 1 &> v_vcf2genome.txt || true
mtnucratio -Xmx${task.memory.toGiga()}g --help &> v_mtnucratiocalculator.txt || true
sexdeterrmine --version &> v_sexdeterrmine.txt || true
kraken2 --version | head -n 1 &> v_kraken.txt || true
endorS.py --version &> v_endorSpy.txt || true
pileupCaller --version &> v_sequencetools.txt 2>&1 || true
bowtie2 --version | grep -a 'bowtie2-.* -fdebug' > v_bowtie2.txt || true
eigenstrat_snp_coverage --version | cut -d ' ' -f2 >v_eigenstrat_snp_coverage.txt || true
mapDamage --version > v_mapdamage.txt || true
bbduk.sh | grep 'Last modified' | cut -d ' ' -f 3-99 > v_bbduk.txt || true
bbversion.sh > v_bbduk.txt || true
bcftools --version | grep 'bcftools' | cut -d ' ' -f 2 > v_bcftools.txt || true
scrape_software_versions.py &> software_versions_mqc.yaml
"""
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