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Update to new container links in CI config
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samuell committed Feb 13, 2024
1 parent 0b389dc commit 49c6e94
Showing 1 changed file with 8 additions and 8 deletions.
16 changes: 8 additions & 8 deletions configs/nextflow.ci.config
Original file line number Diff line number Diff line change
Expand Up @@ -72,10 +72,10 @@ process {
cpus=2

withName: amrfinderplus {
container = "${params.containerDir}/amrfinderplus.sif"
container = "${params.containerDir}/ncbi-amrfinderplus.sif"
cpus = 4
memory = '10 GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/amrfinderplus", mode: 'copy', overwrite: true ]
publishDir = [ path: "${params.outdir}/${params.speciesDir}/ncbi-amrfinderplus", mode: 'copy', overwrite: true ]
ext.args = "--plus"
}
withName: assembly_trim_clean {
Expand Down Expand Up @@ -118,11 +118,11 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/cron", mode: 'copy', overwrite: true, pattern: '*.json' ]
}
withName: create_analysis_result {
container = "${params.containerDir}/pythonScripts.sif"
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
}
withName: create_cdm_input {
container = "${params.containerDir}/pythonScripts.sif"
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/cdm_input", mode: 'copy', overwrite: true ]
}
withName: export_to_cdm {
Expand Down Expand Up @@ -153,7 +153,7 @@ process {
ext.args = "--species tb --format csv"
}
withName: post_align_qc {
container = "${params.containerDir}/postAlignQc.sif"
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
}
withName: quast {
Expand All @@ -171,7 +171,7 @@ process {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/samtools", mode: 'copy', overwrite: true ]
}
withName: save_analysis_metadata {
container = "${params.containerDir}/pythonScripts.sif"
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
}
withName: snippy {
Expand Down Expand Up @@ -210,12 +210,12 @@ process {
}
withName: tbprofiler_tbdb {
memory = '10 GB'
container = "${params.containerDir}/tbprofiler.sif"
container = "${params.containerDir}/tb-profiler.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_tbdb", mode: 'copy', overwrite: true ]
}
withName: tbprofiler_who {
memory = '10 GB'
container = "${params.containerDir}/tbprofiler.sif"
container = "${params.containerDir}/tb-profiler.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_who", mode: 'copy', overwrite: true ]
}
withName: virulencefinder {
Expand Down

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