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GATK4 first round without MuTect1 and indel realignment #607

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maxulysse merged 41 commits into from
Aug 14, 2018
Merged

GATK4 first round without MuTect1 and indel realignment #607

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c9b2cd9
QR for posters
Jul 5, 2018
428c893
Dockerand singularity images for vcfanno
Jul 5, 2018
6f438ad
removing superfluous routines, adding comments
Jul 6, 2018
e00872b
logging improvements
Jul 6, 2018
f6c60bf
nfcore based image file containing vcfanno and qc modules also
Jul 6, 2018
a3f102d
on a way to unify to nf-core and GATK4
Jul 9, 2018
576c171
It works without indelrealignment until CreateRecalibrationTable
Jul 9, 2018
0aea380
new target directories for Prerocessing, works to the end of ApplyBQSR
Jul 9, 2018
72a1b50
HaplotypeCaller works with GATK4
Jul 10, 2018
c6137bf
path and version fixed for both manta and strelka
Jul 10, 2018
bba73f1
Mutect2 GATK4 initial dumb version
Jul 11, 2018
70a3584
Added genome index file
Jul 11, 2018
a836057
Changed Dockerfile to follow https://github.com/nf-core/methylseq/pul…
Jul 11, 2018
733e2c4
removed -Xmx4g because it was ignored anyway and made a syntax/workfl…
Jul 11, 2018
449f939
alphabetical order and added freebayes and new htslib version
Jul 11, 2018
3fb6dc6
freebayes and igvtools in the core container
Jul 11, 2018
0c71f0a
set -euo pipefail needed also for germline
Jul 12, 2018
da3be40
die mutect1
Jul 12, 2018
4db0d5d
commenting out AFs as it will be for a new sprint
Jul 17, 2018
efd11c6
vcfanno is merged to the core
Jul 17, 2018
e81e100
removed igvtools (as went to core)
Jul 17, 2018
0876a89
Merge remote-tracking branch 'upstream/master'
Jul 27, 2018
7cf77b6
Not using the log util, as it is not working
Jul 30, 2018
e2cacd7
fixed indent
Jul 31, 2018
735463b
gatk-launch rename
Jul 31, 2018
a64dd3c
MarkDuplicates got all the memory
Jul 31, 2018
c14fa8e
Merge branch 'master' of github.com:szilvajuhos/Sarek
Jul 31, 2018
5ab4491
Latest versions
Aug 1, 2018
537faa8
MarkDuplicates MAX_RECORDS_IN_RAM decreased to 50000
Aug 1, 2018
24b1ffb
Picard removed from buildReferences.nf
Aug 1, 2018
a5b3f7c
adding all the cpus and mem to MarkDuplicates
Aug 1, 2018
6ebed7a
update submodule Sarek-data a.k.a. #609
Aug 2, 2018
58bab13
s/gatk-launch/gatk/
Aug 2, 2018
12826fd
removing realign parts
Aug 2, 2018
b21dc68
removing realign parts
Aug 2, 2018
db137ce
small review changes
Aug 2, 2018
cb7e228
Merge branch 'master' of github.com:szilvajuhos/Sarek
Aug 2, 2018
97d3fc5
adding singularty environments for tests
Aug 4, 2018
98cf879
VEP fancy parametrisation
Aug 4, 2018
393da8b
memory adjustments for samtools and MarkDuplicates
Aug 14, 2018
9d20c68
s/sarek-core/sarek/ also deleting build.sh
Aug 14, 2018
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13 changes: 8 additions & 5 deletions annotate.nf
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Expand Up @@ -73,23 +73,23 @@ vcfToAnnotate = Channel.create()
vcfNotToAnnotate = Channel.create()

if (annotateVCF == []) {
// by default we annotate both germline and somatic results that we can find in the VariantCalling directory
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@maxulysse maxulysse Jul 17, 2018

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In fact, we annote all available vcfs by default, so it's not really a question of germline/somatic, but really more a question of which tools was run

Channel.empty().mix(
Channel.fromPath("${directoryMap.haplotypecaller}/*.vcf.gz")
.flatten().map{vcf -> ['haplotypecaller', vcf]},
Channel.fromPath("${directoryMap.manta}/*SV.vcf.gz")
.flatten().map{vcf -> ['manta', vcf]},
Channel.fromPath("${directoryMap.mutect1}/*.vcf.gz")
.flatten().map{vcf -> ['mutect1', vcf]},
Channel.fromPath("${directoryMap.mutect2}/*.vcf.gz")
.flatten().map{vcf -> ['mutect2', vcf]},
Channel.fromPath("${directoryMap.strelka}/*{somatic,variants}*.vcf.gz")
Channel.fromPath("${directoryMap.strelka}/*{somatic,variants}*.vcf.gz") // Strelka only
.flatten().map{vcf -> ['strelka', vcf]},
Channel.fromPath("${directoryMap.strelkabp}/*{somatic,variants}*.vcf.gz")
Channel.fromPath("${directoryMap.strelkabp}/*{somatic,variants}*.vcf.gz") // Strelka with Manta indel candidates
.flatten().map{vcf -> ['strelkabp', vcf]}
).choice(vcfToAnnotate, vcfNotToAnnotate) {
annotateTools == [] || (annotateTools != [] && it[0] in annotateTools) ? 0 : 1
}
} else if (annotateTools == []) {
// alternatively, annotate user-submitted VCFs
list = ""
annotateVCF.each{ list += ",${it}" }
list = list.substring(1)
Expand All @@ -101,6 +101,10 @@ if (annotateVCF == []) {

vcfNotToAnnotate.close()

// as now have the list of VCFs to annotate, the first step is to annotate with allele frequencies, if there are any



(vcfForBCFtools, vcfForVCFtools, vcfForSnpeff, vcfForVep) = vcfToAnnotate.into(4)

vcfForVep = vcfForVep.map {
Expand Down Expand Up @@ -346,7 +350,6 @@ def helpMessage() {
log.info " Possible values are:"
log.info " haplotypecaller (Annotate HaplotypeCaller output)"
log.info " manta (Annotate Manta output)"
log.info " mutect1 (Annotate MuTect1 output)"
log.info " mutect2 (Annotate MuTect2 output)"
log.info " strelka (Annotate Strelka output)"
log.info " --annotateVCF"
Expand Down
10 changes: 1 addition & 9 deletions buildContainers.nf
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Expand Up @@ -177,13 +177,6 @@ def grabRevision() {
def defineContainersList(){
// Return list of authorized containers
return [
'freebayes',
'gatk',
'gatk4',
'igvtools',
'mutect1',
'picard',
'qctools',
'r-base',
'runallelecount',
'sarek',
Expand All @@ -208,8 +201,7 @@ def helpMessage() {
log.info " --containers: Choose which containers to build"
log.info " Default: all"
log.info " Possible values:"
log.info " all, freebayes, gatk, gatk4, igvtools, mutect1, picard"
log.info " qctools, r-base, runallelecount, sarek, snpeff"
log.info " all, r-base, runallelecount, sarek, snpeff"
log.info " snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38"
log.info " --docker: Build containers using Docker"
log.info " --help"
Expand Down
2 changes: 1 addition & 1 deletion buildReferences.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ process BuildVCFIndex {

script:
"""
\$IGVTOOLS_HOME/igvtools index ${f_reference}
igvtools index ${f_reference}
"""
}

Expand Down
39 changes: 18 additions & 21 deletions configuration/containers.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,50 +11,47 @@ process {
$BuildBWAindexes.container = "${params.repository}/sarek:${params.tag}"
$BuildPicardIndex.container = "${params.repository}/picard:${params.tag}"
$BuildSAMToolsIndex.container = "${params.repository}/sarek:${params.tag}"
$BuildVCFIndex.container = "${params.repository}/igvtools:${params.tag}"
$BuildVCFIndex.container = "${params.repository}/sarek:${params.tag}"
$CompressVCF.container = "${params.repository}/sarek:${params.tag}"
$ConcatVCF.container = "${params.repository}/sarek:${params.tag}"
$CreateRecalibrationTable.container = "${params.repository}/gatk:${params.tag}"
$GetVersionAll.container = "${params.repository}/qctools:${params.tag}"
$CreateRecalibrationTable.container = "${params.repository}/sarek:${params.tag}"
$GetVersionAll.container = "${params.repository}/sarek:${params.tag}"
$GetVersionAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
$GetVersionASCAT.container = "${params.repository}/r-base:${params.tag}"
$GetVersionBamQC.container = "${params.repository}/qctools:${params.tag}"
$GetVersionBamQC.container = "${params.repository}/sarek:${params.tag}"
$GetVersionBCFtools.container = "${params.repository}/sarek:${params.tag}"
$GetVersionBWAsamtools.container = "${params.repository}/sarek:${params.tag}"
$GetVersionFastQC.container = "${params.repository}/qctools:${params.tag}"
$GetVersionFreeBayes.container = "${params.repository}/freebayes:${params.tag}"
$GetVersionGATK.container = "${params.repository}/gatk:${params.tag}"
$GetVersionFastQC.container = "${params.repository}/sarek:${params.tag}"
$GetVersionFreeBayes.container = "${params.repository}/sarek:${params.tag}"
$GetVersionGATK.container = "${params.repository}/sarek:${params.tag}"
$GetVersionManta.container = "${params.repository}/sarek:${params.tag}"
$GetVersionPicard.container = "${params.repository}/picard:${params.tag}"
$GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
$GetVersionStrelka.container = "${params.repository}/sarek:${params.tag}"
$GetVersionVCFtools.container = "${params.repository}/qctools:${params.tag}"
$GetVersionVCFtools.container = "${params.repository}/sarek:${params.tag}"
$GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
$IndelRealigner.container = "${params.repository}/gatk:${params.tag}"
$MapReads.container = "${params.repository}/sarek:${params.tag}"
$MarkDuplicates.container = "${params.repository}/picard:${params.tag}"
$MarkDuplicates.container = "${params.repository}/sarek:${params.tag}"
$MergeBams.container = "${params.repository}/sarek:${params.tag}"
$RealignerTargetCreator.container = "${params.repository}/gatk:${params.tag}"
$RecalibrateBam.container = "${params.repository}/gatk:${params.tag}"
$RecalibrateBam.container = "${params.repository}/sarek:${params.tag}"
$RunAlleleCount.container = "${params.repository}/runallelecount:${params.tag}"
$RunAscat.container = "${params.repository}/r-base:${params.tag}"
$RunBamQC.container = "${params.repository}/qctools:${params.tag}"
$RunBamQC.container = "${params.repository}/sarek:${params.tag}"
$RunBcftoolsStats.container = "${params.repository}/sarek:${params.tag}"
$RunConvertAlleleCounts.container = "${params.repository}/r-base:${params.tag}"
$RunFastQC.container = "${params.repository}/qctools:${params.tag}"
$RunFreeBayes.container = "${params.repository}/freebayes:${params.tag}"
$RunGenotypeGVCFs.container = "${params.repository}/gatk:${params.tag}"
$RunHaplotypecaller.container = "${params.repository}/gatk:${params.tag}"
$RunFastQC.container = "${params.repository}/sarek:${params.tag}"
$RunFreeBayes.container = "${params.repository}/sarek:${params.tag}"
$RunGenotypeGVCFs.container = "${params.repository}/sarek:${params.tag}"
$RunHaplotypecaller.container = "${params.repository}/sarek:${params.tag}"
$RunManta.container = "${params.repository}/sarek:${params.tag}"
$RunMultiQC.container = "${params.repository}/qctools:${params.tag}"
$RunMutect1.container = "${params.repository}/mutect1:${params.tag}"
$RunMutect2.container = "${params.repository}/gatk:${params.tag}"
$RunMultiQC.container = "${params.repository}/sarek:${params.tag}"
$RunMutect2.container = "${params.repository}/sarek:${params.tag}"
$RunSamtoolsStats.container = "${params.repository}/sarek:${params.tag}"
$RunSingleManta.container = "${params.repository}/sarek:${params.tag}"
$RunSingleStrelka.container = "${params.repository}/sarek:${params.tag}"
$RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.repository}/snpeffgrch38:${params.tag}" : "${params.repository}/snpeffgrch37:${params.tag}"}
$RunStrelka.container = "${params.repository}/sarek:${params.tag}"
$RunStrelkaBP.container = "${params.repository}/sarek:${params.tag}"
$RunVcftools.container = "${params.repository}/qctools:${params.tag}"
$RunVcftools.container = "${params.repository}/sarek:${params.tag}"
$RunVEP.container = {params.genome == 'GRCh38' ? "${params.repository}/vepgrch38:${params.tag}" : "${params.repository}/vepgrch37:${params.tag}"}
}
3 changes: 3 additions & 0 deletions configuration/genomes.config
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Expand Up @@ -42,6 +42,9 @@ params {
knownIndels = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
knownIndelsIndex = "${params.genome_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
snpeffDb = "GRCh38.86"
// This a nasty-looking list of allele-frequencies files. Add/remove files to match to your sets
//AF_files = "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf"
//AF_indexes = "${params.genome_base}/{00-All.dbsnp_151.hg38.CAF.TOPMED.alternate.allele.freq,hapmap_3.3_grch38_pop_stratified_af.HMAF,SweGen_hg38_stratified.SWAF}.vcf.idx"
}
'smallGRCh37' {
acLoci = "${params.genome_base}/1000G_phase3_20130502_SNP_maf0.3.small.loci"
Expand Down
44 changes: 21 additions & 23 deletions configuration/singularity-path.config
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Expand Up @@ -14,52 +14,50 @@ singularity {

process {
$BuildBWAindexes.container = "${params.containerPath}/sarek-${params.tag}.img"
$BuildPicardIndex.container = "${params.containerPath}/picard-${params.tag}.img"
$BuildPicardIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
$BuildSAMToolsIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
$BuildVCFIndex.container = "${params.containerPath}/igvtools-${params.tag}.img"
$BuildVCFIndex.container = "${params.containerPath}/sarek-${params.tag}.img"
$CompressVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
$ConcatVCF.container = "${params.containerPath}/sarek-${params.tag}.img"
$CreateRecalibrationTable.container = "${params.containerPath}/gatk-${params.tag}.img"
$GetVersionAll.container = "${params.containerPath}/qctools-${params.tag}.img"
$CreateRecalibrationTable.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionAll.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
$GetVersionASCAT.container = "${params.containerPath}/r-base-${params.tag}.img"
$GetVersionBamQC.container = "${params.containerPath}/qctools-${params.tag}.img"
$GetVersionBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionBCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionBWAsamtools.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionFastQC.container = "${params.containerPath}/qctools-${params.tag}.img"
$GetVersionFreeBayes.container = "${params.containerPath}/freebayes-${params.tag}.img"
$GetVersionGATK.container = "${params.containerPath}/gatk-${params.tag}.img"
$GetVersionFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionGATK.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionManta.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionPicard.container = "${params.containerPath}/picard-${params.tag}.img"
$GetVersionSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
$GetVersionStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionVCFtools.container = "${params.containerPath}/qctools-${params.tag}.img"
$GetVersionVCFtools.container = "${params.containerPath}/sarek-${params.tag}.img"
$GetVersionVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
$IndelRealigner.container = "${params.containerPath}/gatk-${params.tag}.img"
$IndelRealigner.container = "${params.containerPath}/sarek-${params.tag}.img"
$MapReads.container = "${params.containerPath}/sarek-${params.tag}.img"
$MarkDuplicates.container = "${params.containerPath}/picard-${params.tag}.img"
$MarkDuplicates.container = "${params.containerPath}/sarek-${params.tag}.img"
$MergeBams.container = "${params.containerPath}/sarek-${params.tag}.img"
$RealignerTargetCreator.container = "${params.containerPath}/gatk-${params.tag}.img"
$RecalibrateBam.container = "${params.containerPath}/gatk-${params.tag}.img"
$RealignerTargetCreator.container = "${params.containerPath}/sarek-${params.tag}.img"
$RecalibrateBam.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunAlleleCount.container = "${params.containerPath}/runallelecount-${params.tag}.img"
$RunAscat.container = "${params.containerPath}/r-base-${params.tag}.img"
$RunBamQC.container = "${params.containerPath}/qctools-${params.tag}.img"
$RunBamQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunBcftoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunConvertAlleleCounts.container = "${params.containerPath}/r-base-${params.tag}.img"
$RunFastQC.container = "${params.containerPath}/qctools-${params.tag}.img"
$RunFreeBayes.container = "${params.containerPath}/freebayes-${params.tag}.img"
$RunGenotypeGVCFs.container = "${params.containerPath}/gatk-${params.tag}.img"
$RunHaplotypecaller.container = "${params.containerPath}/gatk-${params.tag}.img"
$RunFastQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunFreeBayes.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunGenotypeGVCFs.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunHaplotypecaller.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunManta.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunMultiQC.container = "${params.containerPath}/qctools-${params.tag}.img"
$RunMutect1.container = "${params.containerPath}/mutect1-${params.tag}.img"
$RunMutect2.container = "${params.containerPath}/gatk-${params.tag}.img"
$RunMultiQC.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunMutect2.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSamtoolsStats.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSingleManta.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSingleStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunSnpeff.container = {params.genome == 'GRCh38' ? "${params.containerPath}/snpeffgrch38-${params.tag}.img" : "${params.containerPath}/snpeffgrch37-${params.tag}.img"}
$RunStrelka.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunStrelkaBP.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunVcftools.container = "${params.containerPath}/qctools-${params.tag}.img"
$RunVcftools.container = "${params.containerPath}/sarek-${params.tag}.img"
$RunVEP.container = {params.genome == 'GRCh38' ? "${params.containerPath}/vepgrch38-${params.tag}.img" : "${params.containerPath}/vepgrch37-${params.tag}.img"}
}
8 changes: 2 additions & 6 deletions configuration/uppmax-localhost.config
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Expand Up @@ -14,7 +14,7 @@ env {
params {
genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37'
singleCPUMem = 8.GB
totalMemory = 104.GB // change to 240 on irma
totalMemory = 92.GB // change to 240 on irma
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@maxulysse maxulysse Aug 1, 2018

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Why did you change to 92?

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@szilvajuhos szilvajuhos Aug 2, 2018

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by mistake

}

executor {
Expand Down Expand Up @@ -70,7 +70,7 @@ process {
memory = {params.totalMemory}
}
$MarkDuplicates {
memory = {params.singleCPUMem * 2 * task.attempt}
// for deep sequencing we do need all the memory
}
$MergeBams {
cpus = 16
Expand Down Expand Up @@ -117,10 +117,6 @@ process {
}
$RunMultiQC {
}
$RunMutect1 {
cpus = 1
memory = {params.singleCPUMem * task.attempt}
}
$RunMutect2 {
cpus = 1
memory = {params.singleCPUMem * task.attempt}
Expand Down
11 changes: 1 addition & 10 deletions configuration/uppmax-slurm.config
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Expand Up @@ -52,10 +52,7 @@ process {
time = {params.runTime * task.attempt}
}
$MarkDuplicates {
cpus = 1
memory = {params.singleCPUMem * 8 * task.attempt}
queue = 'core'
time = {params.runTime * task.attempt}
// looks like overkill, but for deep sequencing we do need all the memory
}
$MergeBams {
memory = {params.singleCPUMem * task.attempt}
Expand Down Expand Up @@ -116,12 +113,6 @@ process {
$RunMultiQC {
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$RunMutect1 {
queue = 'core'
time = {params.runTime * task.attempt}
cpus = 1
memory = {params.singleCPUMem * task.attempt}
}
$RunMutect2 {
cpus = 1
memory = {params.singleCPUMem * task.attempt}
Expand Down
30 changes: 0 additions & 30 deletions containers/freebayes/Dockerfile
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25 changes: 0 additions & 25 deletions containers/mutect1/Dockerfile
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