add skip_m6a param#135
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Pull request overview
Adds a new --skip_m6a parameter to optionally bypass the Fibertools m6A prediction step in the LRSOMATIC workflow, allowing runs to proceed without generating m6A-tagged BAMs.
Changes:
- Add
params.skip_m6adefault tonextflow.config. - Gate
FIBERTOOLSRS_PREDICTM6Aexecution behind--skip_m6aand ensurepredicted_bamsis still defined in both branches.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
| workflows/lrsomatic.nf | Adds conditional logic to optionally skip m6A prediction while still producing a unified predicted_bams channel. |
| nextflow.config | Introduces a new pipeline parameter skip_m6a with default false. |
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There appears to be an extra whitespace-only line here (blank line with indentation). This can trip whitespace/lint checks and makes diffs noisier; please remove trailing whitespace / keep blank lines empty.
Suggested change
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| if (!params.skip_m6a){ | ||
| FIBERTOOLSRS_PREDICTM6A ( | ||
| pacbio_bams.kinetics | ||
| ) | ||
| pacbio_bams.noKinetics | ||
| .mix(FIBERTOOLSRS_PREDICTM6A.out.bam) | ||
| .set{predicted_bams} | ||
| } | ||
| else { | ||
| pacbio_bams.noKinetics | ||
| .mix(pacbio_bams.kinetics) | ||
| .set{predicted_bams} | ||
| } |
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This adds a new control-flow branch (--skip_m6a) that bypasses FIBERTOOLSRS_PREDICTM6A. The repo uses nf-test (tests/default.nf.test) but there’s no test case covering this new parameter; please add a second nf-test scenario that runs the pipeline with --skip_m6a to ensure the workflow still completes and produces expected outputs when m6A prediction is disabled.
| skip_ascat = false | ||
| skip_wakhan = false | ||
| skip_fiber = false | ||
| skip_m6a = false |
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New params.skip_m6a is added here, but it isn’t represented in nextflow_schema.json under $defs.skip_options.properties (where the other skip_* params are defined). This means --help/schema validation and generated docs won’t expose the option; please add skip_m6a to the schema (and update usage docs if they’re generated from it).
Suggested change
| skip_m6a = false |
| FIBERTOOLSRS_PREDICTM6A ( | ||
| pacbio_bams.kinetics | ||
| ) | ||
| if (!params.skip_m6a){ |
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Spacing is inconsistent with the surrounding style (if (!params.skip_fiber) { etc.): if (!params.skip_m6a){ is missing a space before {. Please align formatting to the existing style to keep the workflow readable and reduce diff noise in future changes.
Suggested change
| if (!params.skip_m6a){ | |
| if (!params.skip_m6a) { |
ljwharbers
approved these changes
Mar 12, 2026
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).