Merge branch 'dev' into patch-testconfig_params_updates

Author: jfy133

CHANGELOG.md

@@ -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)
 - [#889](https://github.com/nf-core/eager/issues/889) Remove/updated parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
 
 ### `Dependencies`

main.nf

@@ -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
     """