Massive conda update #1663
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Massive conda update #1663
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maxulysse
commented
Sep 23, 2024
|
edmundmiller
approved these changes
Oct 3, 2024
Good for me then |
| @@ -64,12 +64,12 @@ process { | |||
| // BCFTOOLS ANNOTATE | |||
| if (params.tools && params.tools.split(',').contains('bcfann')) { | |||
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// ALL ANNOTATION TOOLS
if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge') || params.tools.split(',').contains('bcfann'))) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
ext.prefix = { input.name - '.vcf' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
pattern: "*{gz.tbi}"
]
}
}
if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
pattern: "*{gz,gz.tbi}",
saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
]
}
}
```
This could be cleaned up I think?
| @@ -50,7 +50,10 @@ workflow FASTQ_CREATE_UMI_CONSENSUS_FGBIO { | |||
| // Using newly created groups | |||
| // To call a consensus across reads in the same group | |||
| // And emit a consensus BAM file | |||
| CALLUMICONSENSUS(GROUPREADSBYUMI.out.bam) | |||
| // TODO: add params for call_min_reads and call_min_baseq | |||
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Should be an issue
| @@ -38,12 +45,13 @@ process DEEPVARIANT { | |||
| --output_gvcf=${prefix}.g.vcf.gz \\ | |||
| ${args} \\ | |||
| ${regions} \\ | |||
| --intermediate_results_dir=. \\ | |||
| ${par_regions} \\ | |||
| --intermediate_results_dir=tmp \\ | |||
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are we sure about this one? If nextflow starts writing to /tmp here againit will break a lot of cluster. The . should ensure it writes to the current scratch directory
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I'll update the module upstream
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It should not write to /tmp, it should write to a directory tmp in the work/scratch directory.
Comment on lines
+12
to
+16
| tuple val(meta), path(input), path(input_index), path(intervals), path(recal_table) | ||
| tuple val(meta1), path(fasta) | ||
| tuple val(meta2), path(fai) | ||
| tuple val(meta3), path(dbsnp) | ||
| tuple val(meta4), path(dbsnp_tbi) |
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Did you test this? I am surprised this didn't require changes to the module call in bam_variant_calling_germline
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NOT AT ALL, I thought we fixed sentieon server so we could do CI
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🤦
Anyhow, I can see that all sentieon modules are using oras, so we still need to update those one ore time
| echo "Decoded and exported Sentieon test-license system environment variables" | ||
| fi | ||
| sentieon driver $args -t $task.cpus $input_list -r ${fasta} --algo LocusCollector $args2 --fun score_info ${prefix_basename}.score | ||
| sentieon driver $args3 -t $task.cpus $input_list -r ${fasta} --algo Dedup $args4 --score_info ${prefix_basename}.score --metrics ${metrics} ${prefix} |
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We are not using the suffix anymore. think the config here needs updating to have .cram in the prefix end:
sarek/conf/modules/sentieon_dedup.config
Line 19 in 5cc3049
| @@ -64,7 +39,12 @@ process SENTIEON_BWAMEM { | |||
| -t $task.cpus \\ | |||
| \$INDEX \\ | |||
| $reads \\ | |||
| | sentieon util sort -r $fasta -t $task.cpus -o ${prefix}.bam --sam2bam - | |||
| | sentieon util sort -r $fasta -t $task.cpus -o ${prefix} --sam2bam - | |||
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similar here. The prefix already should contain the final file ending. We could consider using cram here already. I assume people would always run sentieon for preprocessing if they have it.
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Replace #1662
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).