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Fix hopper config #389

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Fix hopper config #389

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8c2d7db
Fix hopper config
ryanjameskennedy Jan 27, 2025
879c99d
Update fastqc mem
ryanjameskennedy Jan 27, 2025
6c865d1
Update fastqc mem for all configs
ryanjameskennedy Jan 27, 2025
e454c81
Minor adjustments to formatting of configs
ryanjameskennedy Jan 29, 2025
52d2c8c
Create nextflow.lund.config containing both dev and production profiles
ryanjameskennedy Jan 29, 2025
c057c71
Rename lund config
ryanjameskennedy Jan 29, 2025
9f68521
Update workflow calling system and cmd config
ryanjameskennedy Jan 29, 2025
078dda0
Fix when cmds re workflow.profile
ryanjameskennedy Jan 29, 2025
4b4ee04
Move when commands to config
ryanjameskennedy Jan 29, 2025
4c803fa
Update mem for sccmec
ryanjameskennedy Jan 29, 2025
81eddcb
Fix sccmec versions file
ryanjameskennedy Jan 29, 2025
1aee122
Rm old cmd configs
ryanjameskennedy Jan 29, 2025
b6b5f14
Update when commands in all configs
ryanjameskennedy Jan 30, 2025
b7476b0
Add when operator to all modules not in bacterial base.nf
ryanjameskennedy Jan 30, 2025
b0499ab
Fix handling of ONT samples re fastqc & postalignqc
ryanjameskennedy Jan 30, 2025
707f073
Apply PR #391 changes to configs
ryanjameskennedy Jan 31, 2025
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Added module `fastq` to check qc of strep samples
- Added module `hostile` to remove human reads
- Added module `sccmec` for typing of SCCmec cassettes in assemblies of Staphylococcus species
- Added when operators to all modules that aren't in `bacterial_base.nf`

### Fixed

Expand All @@ -41,6 +42,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Removed serotypefinder from saureus workflow
- Fixed jasen running only on the first row/sample in csv
- Fixed channel problem by changing `Channel.of([])` to `Channel.value([])`
- Fixed `nextflow.hopper.config` re singularity image path
- Fixed sccmec version file
- Fixed handling of ONT samples re fastqc & postalignqc

### Changed

Expand All @@ -59,6 +63,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Changed ska & sourmash filepath to symlink dir in `nextflow.hopper.config` & `nextflow.dev.config`
- Updated Kraken db filepath in `nextflow.hopper.config` & `nextflow.dev.config`
- Changed `staphylococcus_aureus_all` to `saureus_all` in `Makefile`
- Moved all when commands to configs
- Update fastqc & sccmec mem settings

## [0.9.0]

Expand Down
31 changes: 28 additions & 3 deletions configs/nextflow.base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -147,17 +147,20 @@ process {
withName: add_igv_track {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
ext.when = { params.species == "mycobacterium tuberculosis" }
}
withName: amrfinderplus {
container = "${params.containerDir}/ncbi-amrfinderplus.sif"
cpus = 4
memory = '10.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/amrfinderplus", mode: 'copy', overwrite: true ]
ext.args = "--plus"
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: annotate_delly {
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
ext.when = { params.species == "mycobacterium tuberculosis" }
}
withName: assembly_trim_clean {
container = "${params.containerDir}/perl-json.sif"
Expand All @@ -174,29 +177,35 @@ process {
withName: bwa_index {
container = "${params.containerDir}/bwakit.sif"
ext.args = "-M"
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: bwa_mem_dedup {
container = "${params.containerDir}/bwakit.sif"
cpus = 16
memory = '20.GB'
ext.args = "-M"
ext.when = true
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: bwa_mem_ref {
container = "${params.containerDir}/bwakit.sif"
cpus = 16
memory = '20.GB'
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
ext.args = "-M"
ext.when = { params.referenceGenome }
ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
}
withName: chewbbaca_allelecall {
cpus = 16
memory = '12.GB'
container = "${params.containerDir}/chewbbaca.sif"
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: chewbbaca_create_batch_list {
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: chewbbaca_split_results {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: create_analysis_result {
container = "${params.containerDir}/bonsai-prp.sif"
Expand All @@ -216,6 +225,7 @@ process {
withName: emmtyper {
container = "${params.containerDir}/emmtyper.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
ext.when = { params.species in ["streptococcus", "streptococcus pyogenes"] }
}
withName: export_to_cdm {
publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
Expand All @@ -231,6 +241,7 @@ process {
}
withName: fastqc {
cpus = 4
memory = '2.GB'
container = "${params.containerDir}/fastqc.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/fastqc", mode: 'copy', overwrite: true ]
ext.args = "--threads 4"
Expand All @@ -239,6 +250,7 @@ process {
container = "${params.containerDir}/freebayes.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
ext.args = "-C 2 -F 0.2 --pooled-continuous"
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: hostile {
container = "https://depot.galaxyproject.org/singularity/hostile:2.0.0--pyhdfd78af_0"
Expand All @@ -253,24 +265,27 @@ process {
}
withName: mask_polymorph_assembly {
publishDir = [ path: "${params.outdir}/${params.speciesDir}/mask", mode: 'copy', overwrite: true ]
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: medaka {
container = "${params.containerDir}/medaka.sif"
cpus = 20
memory = '32.GB'
time=2.h
publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
ext.args = "--threads 40 -m r941_min_sup_g507"
ext.args = "-t 40 -m r941_min_sup_g507"
}
withName: mlst {
container = "${params.containerDir}/mlst.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: mykrobe {
memory = '4.GB'
container = "${params.containerDir}/mykrobe.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
ext.args = "--species tb --format csv"
ext.when = { params.species == "mycobacterium tuberculosis" }
}
withName: nanoplot {
container = "${params.containerDir}/nanoplot.sif"
Expand All @@ -281,6 +296,7 @@ process {
memory = '2.GB'
container = "${params.containerDir}/bonsai-prp.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
ext.when = { params.species != "streptococcus" }
}
withName: quast {
container = "${params.containerDir}/quast.sif"
Expand All @@ -289,17 +305,20 @@ process {
withName: resfinder {
container = "${params.containerDir}/resfinder.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/resfinder", mode: 'copy', overwrite: true ]
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: samtools_index_assembly {
cpus = 16
memory = '2.GB'
container = "${params.containerDir}/samtools.sif"
ext.when = { params.species != "mycobacterium tuberculosis" }
}
withName: samtools_index_ref {
cpus = 16
memory = '2.GB'
container = "${params.containerDir}/samtools.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
}
withName: save_analysis_metadata {
container = "${params.containerDir}/bonsai-prp.sif"
Expand All @@ -308,6 +327,7 @@ process {
withName: sccmec {
container = "${params.containerDir}/sccmec.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
ext.when = { params.species == "staphylococcus aureus" }
}
withName: seqtk_sample {
container = "${params.containerDir}/seqtk.sif"
Expand All @@ -318,11 +338,13 @@ process {
cpus = 2
container = "${params.containerDir}/serotypefinder.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/serotypefinder", mode: 'copy', overwrite: true ]
ext.when = { (params.species in ["escherichia coli", "klebsiella pneumoniae"]) }
}
withName: shigapass {
cpus = 2
container = "${params.containerDir}/shigapass.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/shigapass", mode: 'copy', overwrite: true ]
ext.when = { params.species == "escherichia coli" }
}
withName: ska_build {
container = "${params.containerDir}/ska2.sif"
Expand All @@ -344,6 +366,7 @@ process {
memory = '32.GB'
container = "${params.containerDir}/snippy.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
ext.when = { params.species == "mycobacterium tuberculosis" }
}
withName: sourmash {
container = "${params.containerDir}/sourmash.sif"
Expand Down Expand Up @@ -371,11 +394,13 @@ process {
container = "${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 ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
ext.when = { params.species == "mycobacterium tuberculosis" }
}
withName: virulencefinder {
cpus = 2
container = "${params.containerDir}/virulencefinder.sif"
publishDir = [ path: "${params.outdir}/${params.speciesDir}/virulencefinder", mode: 'copy', overwrite: true ]
ext.when = { params.species != "mycobacterium tuberculosis" }
}
}

Expand Down
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