Add CADD annotation #266
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Add CADD annotation #266
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jemten
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modules/nf-core/cadd/cadd.diff
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| Changes in module 'nf-core/cadd' | ||
| --- modules/nf-core/cadd/main.nf | ||
| +++ modules/nf-core/cadd/main.nf | ||
| @@ -43,7 +43,7 @@ | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def VERSION = "1.6.post1" // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. | ||
| """ | ||
| - touch ${prefix}.tsv.gz | ||
| + echo "" | gzip > ${prefix}.tsv.gz | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
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| ************************************************************ |
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are these changes that we should try to add to the nf-core module as well?
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Probably, I'll remove them from here for now.
conf/modules/annotate_cadd.config
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| } | ||
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| withName: '.*:ANNOTATE_CADD:BCFTOOLS_VIEW' { | ||
| ext.args = { "--output-type z --types indels,other" } |
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Just out of curiosity, how big are the indels in the SNV/INDEL vcf coming from ONT data? Can they be several 10s of kb and would that severely affect how long it takes to run CADD?
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I haven't tested this yet, will do before merging.
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Added a workaround for references with chr, seems like CADD only scores 1-22,X,Y,M anyway (?) so this should be fine I think:
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jemten
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Aug 9, 2024
nextflow_schema.json
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| "cadd_prescored": { | ||
| "type": "string", | ||
| "exists": true, | ||
| "format": "directory-path", | ||
| "fa_icon": "fas fa-file", | ||
| "description": "Path to the directory containing cadd prescored files.", | ||
| "help_text": "This folder contains the compressed files and indexes that would otherwise be in data/prescored folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation." |
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Should we indicate that, as written currently, this file is only used to score the known indels. Might be worth clarifying that this is not the prescored snv file.
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
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Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
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Closes #265
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).