add replicates, perform QC on individual replicates before merge#138
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ljwharbers merged 7 commits intodevfrom Mar 12, 2026
Merged
add replicates, perform QC on individual replicates before merge#138ljwharbers merged 7 commits intodevfrom
ljwharbers merged 7 commits intodevfrom
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Pull request overview
This PR introduces replicate awareness to the lrsomatic Nextflow pipeline, aiming to run QC on individual replicates before merging them for downstream analysis.
Changes:
- Extend samplesheet/schema parsing to carry
tumor_replicate/normal_replicateand propagate a unifiedmeta.replicate. - Run CRAMINO QC earlier (intended per-replicate) and publish CRAMINO_PRE outputs into replicate-specific directories.
- Update nf-test snapshot outputs to reflect replicate-specific QC directories and an added multi-replicate sample case.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/lrsomatic.nf | Adds replicate to meta, moves CRAMINO_PRE earlier, attempts to strip replicate before merge/concat. |
| subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf | Parses new replicate columns and populates meta.replicate. |
| conf/modules.config | Updates CRAMINO_PRE publishDir to include replicate in the output path. |
| assets/schema_input.json | Adds tumor_replicate and normal_replicate fields with defaults. |
| tests/default.nf.test.snap | Updates expected outputs for replicate-specific QC directories and new sample outputs. |
Comments suppressed due to low confidence (1)
workflows/lrsomatic.nf:188
- After stripping
replicatefrommeta, the channel is not regrouped, so replicate rows will continue through as separate items (andSAMTOOLS_CATwill never seebam.size() > 1). This can lead to duplicate downstream processing and incorrect tumor/normal pairing in latergroupTuple(size: 2)logic. Regroup by the replicate-free meta (e.g.,groupTuple()then flatten) before branching/concatenation so replicates are merged into a single BAM list/file per sample/type.
ch_samplesheet
.map{ meta, bam ->
def new_meta = meta.subMap('id',
'paired_data',
'type',
'platform',
'sex',
'fiber',
'clair3_model',
'clairS_model',
'clairSTO_model',
'kinetics')
return[new_meta, bam]
}
.set{ch_samplesheet_no_rep}
// ch_samplesheet -> meta: [id, paired_data, platform, sex, type, fiber, basecall_model]
// bam: list of unaligned bams
ch_split = ch_samplesheet_no_rep
.branch { meta, bam ->
single: bam.size() == 1
multiple: bam.size() > 1
}
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workflows/lrsomatic.nf
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| downloaded_clair3_models = PREPARE_REFERENCE_FILES.out.downloaded_clair3_models | ||
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| ch_samplesheet.view() |
There was a problem hiding this comment.
ch_samplesheet.view() looks like a debugging statement and will spam logs / potentially expose input paths in normal runs. Consider removing it or gating behind a dedicated debug/trace parameter.
Suggested change
| ch_samplesheet.view() | |
| if (params.trace_samplesheet) { | |
| ch_samplesheet.view() | |
| } |
workflows/lrsomatic.nf
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| .mix ( ch_split.single ) | ||
| .set { ch_cat_ubams } | ||
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| ch_cat_ubams.view() |
There was a problem hiding this comment.
ch_cat_ubams.view() looks like a debugging statement and will spam logs / potentially expose input paths in normal runs. Consider removing it or gating behind a dedicated debug/trace parameter.
Suggested change
| ch_cat_ubams.view() | |
| if( params.debug ) { | |
| ch_cat_ubams.view() | |
| } |
workflows/lrsomatic.nf
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| include { MINIMAP2_INDEX } from '../modules/nf-core/minimap2/index/main' | ||
| include { MINIMAP2_ALIGN } from '../modules/nf-core/minimap2/align/main' | ||
| include { CRAMINO as CRAMINO_PRE } from '../modules/local/cramino/main' | ||
| include { CRAMINO as CRAMINO_PRE_REPLICATES } from '../modules/local/cramino/main' |
There was a problem hiding this comment.
CRAMINO_PRE_REPLICATES is imported but never used. Please remove the unused include or switch the per-replicate QC invocation to use this alias (and keep CRAMINO_PRE for any non-replicate use) to avoid confusion and potential lint failures.
Suggested change
| include { CRAMINO as CRAMINO_PRE_REPLICATES } from '../modules/local/cramino/main' |
| .map { meta, bam_tumor, bam_normal -> | ||
| [ meta, bam_tumor.flatten(), bam_normal.flatten() ] | ||
| } | ||
| .view() |
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The .view() call in PIPELINE_INITIALISATION appears to be left-over debugging and will print samplesheet entries (including file paths) to stdout for every run. Consider removing it or gating it behind a debug/trace parameter.
Suggested change
| .view() |
ljwharbers
approved these changes
Mar 12, 2026
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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).