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Fix fastqc samplenames in multiqc report #638

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merged 4 commits into from
Oct 22, 2024
Merged

Fix fastqc samplenames in multiqc report #638

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d70f9a1
fix samplenames in multiqc report
ramprasadn Oct 21, 2024
7906d3c
update changelog
ramprasadn Oct 21, 2024
2839ae0
update changelog
ramprasadn Oct 21, 2024
4c0d58a
Merge branch 'dev' into fix_fastqc_samplenames
ramprasadn Oct 21, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638)
- Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
- Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
- Update output file name prefix for upd and chromograph to sample-based [#620](https://github.com/nf-core/raredisease/pull/620)
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2 changes: 1 addition & 1 deletion assets/multiqc_config.yml
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Expand Up @@ -44,6 +44,6 @@ module_order:
extra_fn_clean_exts:
- "_sorted_md"
- type: regex
pattern: "_T[0-9]"
pattern: "_LNUMBER[0-9]{1,}"

disable_version_detection: true
2 changes: 1 addition & 1 deletion subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
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Expand Up @@ -97,7 +97,7 @@ workflow PIPELINE_INITIALISATION {
}
.combine( ch_input_counts )
.map { lineno, meta, fastqs -> //append line number to sampleid
new_meta = meta + [id:meta.id+"_T"+lineno[fastqs]]
new_meta = meta + [id:meta.id+"_LNUMBER"+lineno[fastqs]]
return [ new_meta, fastqs ]
}
.set { ch_samplesheet }
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