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Samplesheet checks and parameter conventions (Issue #69) - #82

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Samplesheet checks and parameter conventions (Issue #69)#82
MaximilianStammnitz wants to merge 8 commits into
nf-core:devfrom
MaximilianStammnitz:dev

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@MaximilianStammnitz MaximilianStammnitz commented Oct 18, 2026 •
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Addresses the parameter and samplesheet points of the v1.0.0 release review (#54) and closes issue #69.

Samplesheet

  • assets/schema_input.json: paired-end FASTQ only (BAM and single-end rows are now rejected instead of being silently dropped), type limited to input/output/wildtype, no duplicate sample/type/replicate rows. Single-end support is tracked in Single-end read mode #81 for v1.1.0.
  • The samplesheet is read with samplesheetToList(); meta.id keeps its <sample>_<type>_<replicate>_pe format.
  • New start-up checks in PIPELINE_INITIALISATION:
    • one biological sample per run
    • with --fitness: matching input and output replicate numbers
    • with --error_correction wildtype: exactly one wildtype library
    • --reading_frame: a multiple of 3 and within the reference
    • --mutagenesis_type custom requires --custom_codon_library

Fitness thresholds

  • --min_counts (default 10) is now only the minimum number of reads a variant needs in every input replicate to receive a fitness estimate. As in DiMSum, it is applied to codon variants before synonymous codons are merged, so the default estimator, DiMSum (--fitnessMinInputCountAll) and mutscan analyse the same variants.
  • Variant counting, error correction, the count heatmaps and the SeqDepth curve no longer filter by --min_counts; the error correction therefore always sees every false double.
  • New --output_pseudocount (default 1, the previous behaviour; 0 disables), also passed to DiMSum (--fitnessDropoutPseudocount).

Parameters, schema and config

  • iGenomes removed (genome, igenomes_*, conf/igenomes*.config, getGenomeAttribute()); fasta = null declared; igenomes skipped as a template feature.
  • fitness/dimsum/mutscan are booleans (default false); mutagenesis_type is an enum; custom_codon_library defaults to null instead of '/NULL'.
  • Schema grouped into reference/library, variant counting, error correction, library QC and fitness options.
  • params.publish_dir_mode for every publishDir; overwrite: false and the duplicate summary-report block removed; no publishDir inside modules.
  • COUNTS_TO_FITNESS runs only with --fitness; its tables are published only with --dimsum.
  • --run_seqdepth keeps its positive form (default true) on purpose.

Testing

  • nf-core pipelines lint --release (tools 4.1.0): 0 failures. nextflow lint: no new errors or warnings.
  • The start-up checks and parameter validation were tested with valid and invalid samplesheets and parameters; the default estimator, the mutscan pre-filter and possible_mutations.R were checked against the previous scripts.
  • The nf-test snapshot changes (count heatmaps and SeqDepth curves are no longer filtered at the test's min_counts = 1, and the fitness filter now acts per input replicate), so we'll need a fresh nf-test test --update-snapshot on this branch.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests! (snapshot update pending)
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors). (not needed)

@MaximilianStammnitz
Samplesheet specification and test updates
9080070
@MaximilianStammnitz
Update .nf-core.yml
b0b8f96
@MaximilianStammnitz
Parameters: repurpose --min_counts, add --output_pseudocount, tidy sc…
1af6f2d 
…hema and config

Fitness thresholds (nf-core#69; release review points 7 and 10)
- --min_counts (default 10) is now only the minimum number of reads a variant
  needs in every input replicate to receive a fitness estimate. As in DiMSum,
  it is applied to codon variants before synonymous codons are merged: the
  default estimator, DiMSum (--fitnessMinInputCountAll) and mutscan analyse
  the same variants
- Variant counting, error correction, the count heatmaps and the SeqDepth
  curve no longer filter by --min_counts (threshold fixed at 1)
- New --output_pseudocount (default 1 = previous behaviour; 0 = dropouts get
  no estimate in that replicate), passed to DiMSum (--fitnessDropoutPseudocount)

Parameters and schema (release review points 1 and 17)
- Remove the iGenomes leftovers (genome, igenomes_*, getGenomeAttribute);
  declare fasta = null
- fitness, dimsum, mutscan: boolean, default false
- mutagenesis_type: enum; custom_codon_library: null default instead of the
  '/NULL' sentinel, file must exist
- Schema grouped into reference/library, variant counting, error correction,
  library QC and fitness options

Config and modules (release review points 8 and 15)
- params.publish_dir_mode for every publishDir; no overwrite: false;
  duplicate VISUALIZATION_SUMMARY_REPORT block removed
- Remove the publishDir inside DMSANALYSIS_PROCESS_VARIANT_COUNTS
- COUNTS_TO_FITNESS runs only with --fitness; its tables are published only
  with --dimsum
- Docs: where --min_counts applies (usage.md) and when the DiMSum input
  tables are published (output.md)
@MaximilianStammnitz
Delete conf/igenomes.config
7f882ec
@MaximilianStammnitz
Delete conf/igenomes_ignored.config
6ad721e
@github-actions

github-actions Bot commented Oct 18, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 22950cf

+| ✅ 243 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in CHANGELOG.md: ## v1.0.0 - [unreleased replace with date on release ]

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-18 17:45:38

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github-actions Bot commented Oct 18, 2026 •
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❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

  • ❌ docker | latest-everything | Shard 1/1

See the full run for details.

@MaximilianStammnitz MaximilianStammnitz mentioned this pull request Oct 18, 2026
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@MaximilianStammnitz

MaximilianStammnitz commented Oct 18, 2026

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@BenjaminWehnert1008 I think just adding a new snapshot would do.

@MaximilianStammnitz MaximilianStammnitz mentioned this pull request Oct 18, 2026
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@BenjaminWehnert1008 BenjaminWehnert1008 Awaiting requested review from BenjaminWehnert1008

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