Refactor to adhere to language server #1912
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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maxulysse
reviewed
Aug 14, 2025
| @@ -117,6 +117,7 @@ process { | |||
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| withName: 'NFCORE_SAREK:SAREK:FASTQ_ALIGN_GATK:CRAM_TO_BAM' { | |||
| ext.when = { params.save_output_as_bam } | |||
| // TODO how to handle this properly? | |||
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ie:
ext.prefix = { "${meta.id}.${meta.prefix}" }
and:
path: { "${params.outdir}/preprocessing/${meta.publish_path}/${meta.id}/" },
maxulysse
reviewed
Aug 14, 2025
| @@ -81,6 +81,7 @@ process { | |||
| } | |||
| } | |||
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| //TODO this needs to be removed/moved | |||
maxulysse
reviewed
Aug 14, 2025
Comment on lines
20
to
22
| if (params.use_gatk_spark) { | ||
| containerOptions = '' | ||
| } |
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do we need this with the profile spark?
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Refactoring code to adhere to the language server
WIP:
PR checklist
nf-core pipelines 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).