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Update memory format in configs
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@ryanjameskennedy
ryanjameskennedy committed Jan 17, 2025
1 parent 83bfe5a commit 3f6c60d
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Showing 5 changed files with 80 additions and 79 deletions.
38 changes: 19 additions & 19 deletions configs/nextflow.base.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ singularity {

process {
time=1.h
memory='1 GB'
memory='1.GB'
cpus=2

withName: add_igv_track {
Expand All @@ -150,7 +150,7 @@ process {
withName: amrfinderplus {
container = "${params.containerDir}/ncbi-amrfinderplus.sif"
cpus = 4
memory = '10 GB'
memory = '10.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/amrfinderplus", mode: 'copy', overwrite: true ]
ext.args = "--plus"
}
Expand All @@ -161,7 +161,7 @@ process {
withName: assembly_trim_clean {
container = "${params.containerDir}/perl-json.sif"
cpus = 4
memory = '10 GB'
memory = '10.GB'
ext.args = "--min_quality 23 --bases_to_trim 400 --min_length 100 -p 1 --nosingletons"
}
withName: bracken {
Expand All @@ -177,21 +177,21 @@ process {
withName: bwa_mem_dedup {
container = "${params.containerDir}/bwakit.sif"
cpus = 16
memory = '20 GB'
memory = '20.GB'
ext.args = "-M"
ext.when = true
}
withName: bwa_mem_ref {
container = "${params.containerDir}/bwakit.sif"
cpus = 16
memory = '20 GB'
memory = '20.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
ext.args = "-M"
ext.when = { params.referenceGenome }
}
withName: chewbbaca_allelecall {
cpus = 16
memory = '12 GB'
memory = '12.GB'
container = "${params.containerDir}/chewbbaca.sif"
}
withName: chewbbaca_split_results {
Expand Down Expand Up @@ -222,7 +222,7 @@ process {
withName: flye {
container = "${params.containerDir}/flye.sif"
cpus = 20
memory = '32 GB'
memory = '32.GB'
time=2.h
publishDir = [ path: "${params.outdir}/${params.speciesDir}/flye", mode: 'copy', overwrite: true ]
ext.args = "--threads 40 --genome-size 2.8m --asm-coverage 50"
Expand All @@ -244,7 +244,7 @@ process {
ext.when = { params.useHostile }
}
withName: kraken {
memory = '46 GB'
memory = '46.GB'
cpus = 16
container = "${params.containerDir}/kraken2.sif"
ext.args = "--gzip-compressed"
Expand All @@ -256,7 +256,7 @@ process {
withName: medaka {
container = "${params.containerDir}/medaka.sif"
cpus = 20
memory = '32 GB'
memory = '32.GB'
time=2.h
publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
ext.args = "-t 40 -m r941_min_sup_g507"
Expand All @@ -266,7 +266,7 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
}
withName: mykrobe {
memory = '4 GB'
memory = '4.GB'
container = "${params.containerDir}/mykrobe.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
ext.args = "--species tb --format csv"
Expand All @@ -277,7 +277,7 @@ process {
ext.args = "-t 8"
}
withName: post_align_qc {
memory = '2 GB'
memory = '2.GB'
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
}
Expand All @@ -291,12 +291,12 @@ process {
}
withName: samtools_index_assembly {
cpus = 16
memory = '2 GB'
memory = '2.GB'
container = "${params.containerDir}/samtools.sif"
}
withName: samtools_index_ref {
cpus = 16
memory = '2 GB'
memory = '2.GB'
container = "${params.containerDir}/samtools.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
}
Expand All @@ -322,21 +322,21 @@ process {
withName: ska_build {
container = "${params.containerDir}/ska2.sif"
cpus = 2
memory = '10 GB'
memory = '10.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
ext.args = "-k 31 --threads 1"
}
withName: skesa {
container = "${params.containerDir}/skesa.sif"
cpus = 16
memory = '32 GB'
memory = '32.GB'
time=2.h
publishDir = [ path: "${params.outdir}/${params.speciesDir}/skesa", mode: 'copy', overwrite: true ]
ext.args = "--cores 16 --memory 32"
ext.when = { params.useSkesa }
}
withName: snippy {
memory = '32 GB'
memory = '32.GB'
container = "${params.containerDir}/snippy.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
}
Expand All @@ -348,21 +348,21 @@ process {
withName: spades_illumina {
container = "${params.containerDir}/spades.sif"
cpus = 16
memory = '15 GB'
memory = '15.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_illumina", mode: 'copy', overwrite: true ]
ext.args = "--isolate"
ext.when = { !params.useSkesa }
}
withName: spades_iontorrent {
container = "${params.containerDir}/spades.sif"
cpus = 16
memory = '15 GB'
memory = '15.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_iontorrent", mode: 'copy', overwrite: true ]
ext.args = "--iontorrent --careful --sc"
}
withName: tbprofiler_mergedb {
cpus = 16
memory = '12 GB'
memory = '12.GB'
container = "${params.containerDir}/tb-profiler.sif"
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
Expand Down
34 changes: 17 additions & 17 deletions configs/nextflow.ci.config
View file
Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,7 @@ profiles {

process {
time=1.h
memory='1 GB'
memory='1.GB'
cpus=2

withName: add_igv_track {
Expand All @@ -139,7 +139,7 @@ process {
withName: amrfinderplus {
container = "${params.containerDir}/ncbi-amrfinderplus.sif"
cpus = 4
memory = '10 GB'
memory = '10.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/ncbi-amrfinderplus", mode: 'copy', overwrite: true ]
ext.args = "--plus"
}
Expand All @@ -150,7 +150,7 @@ process {
withName: assembly_trim_clean {
container = "${params.containerDir}/perl-json.sif"
cpus = 4
memory = '10 GB'
memory = '10.GB'
ext.args = "--min_quality 23 --bases_to_trim 400 --min_length 100 -p 1 --nosingletons"
}
withName: bracken {
Expand All @@ -166,21 +166,21 @@ process {
withName: bwa_mem_dedup {
container = "${params.containerDir}/bwakit.sif"
cpus = 4
memory = '12 GB'
memory = '12.GB'
ext.args = "-M"
ext.when = true
}
withName: bwa_mem_ref {
container = "${params.containerDir}/bwakit.sif"
cpus = 4
memory = '12 GB'
memory = '12.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
ext.args = "-M"
ext.when = { params.referenceGenome }
}
withName: chewbbaca_allelecall {
cpus = 4
memory = '12 GB'
memory = '12.GB'
container = "${params.containerDir}/chewbbaca.sif"
}
withName: chewbbaca_split_results {
Expand Down Expand Up @@ -224,7 +224,7 @@ process {
ext.when = { params.useHostile }
}
withName: kraken {
memory = '12 GB'
memory = '12.GB'
cpus = 4
container = "${params.containerDir}/kraken2.sif"
ext.args = "--gzip-compressed"
Expand All @@ -238,7 +238,7 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
}
withName: mykrobe {
memory = '4 GB'
memory = '4.GB'
container = "${params.containerDir}/mykrobe.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
ext.args = "--species tb --format csv"
Expand All @@ -249,7 +249,7 @@ process {
ext.args = "-t 8"
}
withName: post_align_qc {
memory = '2 GB'
memory = '2.GB'
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
}
Expand All @@ -263,12 +263,12 @@ process {
}
withName: samtools_index_assembly {
cpus = 4
memory = '2 GB'
memory = '2.GB'
container = "${params.containerDir}/samtools.sif"
}
withName: samtools_index_ref {
cpus = 4
memory = '2 GB'
memory = '2.GB'
container = "${params.containerDir}/samtools.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
}
Expand All @@ -294,21 +294,21 @@ process {
withName: ska_build {
container = "${params.containerDir}/ska2.sif"
cpus = 2
memory = '10 GB'
memory = '10.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
ext.args = "-k 31 --threads 1"
}
withName: skesa {
container = "${params.containerDir}/skesa.sif"
cpus = 4
memory = '12 GB'
memory = '12.GB'
time=2.h
publishDir = [ path: "${params.outdir}/${params.speciesDir}/skesa", mode: 'copy', overwrite: true ]
ext.args = "--cores 4 --memory 12"
ext.when = { params.useSkesa }
}
withName: snippy {
memory = '12 GB'
memory = '12.GB'
container = "${params.containerDir}/snippy.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
}
Expand All @@ -320,21 +320,21 @@ process {
withName: spades_illumina {
container = "${params.containerDir}/spades.sif"
cpus = 4
memory = '12 GB'
memory = '12.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_illumina", mode: 'copy', overwrite: true ]
ext.args = "--isolate"
ext.when = { !params.useSkesa }
}
withName: spades_iontorrent {
container = "${params.containerDir}/spades.sif"
cpus = 4
memory = '12 GB'
memory = '12.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_iontorrent", mode: 'copy', overwrite: true ]
ext.args = "--iontorrent --careful --sc"
}
withName: tbprofiler_mergedb {
cpus = 4
memory = '12 GB'
memory = '12.GB'
container = "${params.containerDir}/tb-profiler.sif"
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
Expand Down
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