Apply Nextflow 25 strict syntax fixes#1677
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maxulysse
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maxulysse
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Changes to comply with Nextflow strict syntax requirements: Local workflow files (main.nf, subworkflows/local/*, modules/local/*): - Convert `Channel` to `channel` (lowercase) throughout - Replace implicit closure parameter `it` with explicit names - Add `def` keyword to implicit variable declarations - Prefix unused parameters with underscore (_key, _idx, etc.) - Rename variables that shadow input parameters - Move file declarations inside workflow main: blocks - Replace `for` loops with `.each()` functional iteration Config files: - Remove top-level `if (!params.skip_*)` wrappers (strict syntax prohibits top-level conditionals in config files) - Replace implicit closure parameter `it` with explicit `filename` - Convert conditional env assignments to ternary operators See: https://nextflow.io/docs/latest/strict-syntax.html Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Update nf-core components to ensure Nextflow 25 strict syntax compliance. Module changes: - Convert Channel.empty() to channel.empty() - Replace implicit `it` with explicit parameter names - Add `def` to implicit variable declarations - Prefix unused variables with underscore - Many modules switch to topic-based version reporting Modules updated: - bbmap/bbsplit, bracken/bracken, cat/fastq, custom/catadditionalfasta - fastp, gffread, gunzip, hisat2/extractsplicesites, kraken2/kraken2 - rsem/preparereference, rseqc/readdistribution, rseqc/tin - salmon/quant, sentieon/*, sortmerna, sylph/profile - trimgalore, ucsc/bedclip, ucsc/bedgraphtobigwig Subworkflows updated: - bam_dedup_*, bam_markduplicates_picard, bam_sort_stats_samtools - bam_stats_samtools, bedgraph_bedclip_bedgraphtobigwig - fastq_align_hisat2, fastq_fastqc_umitools_*, fastq_qc_trim_filter_* - fastq_remove_rrna, fastq_subsample_fq_salmon, quantify_pseudo_alignment Notable changes from upstream master: - bbmap/bbsplit: topic-based version reporting - fastp: output naming changed from _1/_2 to _R1/_R2 suffix - rseqc/tin: now uses ext.prefix for output naming - sentieon configs: env block syntax for environment variables Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
BBMAP_BBSPLIT changes: - Remove invalid BBMAP_BBSPLIT.out.versions reference (now uses topic channel for versions, collected automatically at workflow level) Sentieon test configuration: - Use null instead of empty string for optional Sentieon env vars to prevent Nextflow warnings about empty environment variable values - Use env block syntax for Sentieon env vars (aligns with nf-core module convention and handles null values from System.getenv() properly) - Create standalone sentieon.config files for each Sentieon test directory with all required settings (process config + env vars) since nf-test doesn't support multiple config files - Remove Sentieon env vars from general test configs to prevent empty env var warnings in non-Sentieon tests Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Update nf-test snapshots to reflect changes from strict syntax updates:
- Topic-based version reporting changes output structure
(versions now reported via topic channel rather than versions.yml)
- Python version now correctly reported in CUSTOM_CATADDITIONALFASTA stub
- RSEM outputs directory changed to ${params.aligner} for consistency
- New RSEM merged output files (merged_genes_long, merged_isoforms_long)
- CUSTOM_CATADDITIONALFASTA now outputs GTF file
- fastp output naming changed from _1/_2 to _R1/_R2 suffix
- rseqc/tin uses ext.prefix for output naming
Module and subworkflow test snapshots updated for all components
modified in previous commits.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add `nextflow lint` to CI to prevent regressions in strict syntax compliance. Changes: - Create separate nextflow-lint.yml workflow for strict syntax validation - Update nf-test.config to use strict syntax (add `=` for assignments) so it no longer needs to be excluded from linting - Disable nf_test_content lint check in .nf-core.yml for strict syntax compatibility (nf-core linting conflicts with some strict syntax patterns) The lint workflow runs on all Nextflow files in the repository. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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maxulysse
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just concerned about tests/bam_input.nf.test.snap
- Fix incorrect nesting of star_rsem/log/ under star_rsem/<SAMPLE>.stat/ - Update log file patterns to match actual STAR output files: - *.SJ.out.tab (splice junctions) - *.Log.final.out (alignment summary) - *.Log.out and *.Log.progress.out (detailed logs) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Thanks @maxulysse ! This is because I fixed something (updated the PR description). The Before: After: Config always applies. Outputs go to Changes:
This is a bug fix - the old behavior was incorrect. |
maxulysse
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Summary
Apply Nextflow 25 strict syntax fixes and update nf-core components for compliance.
Commits
refactor: Apply strict syntax to local files (
ba7caae) -Channel→channel, explicit closure params,defdeclarations, move file declarations insidemain:, remove top-level config conditionalschore: Update nf-core modules/subworkflows (
e192000) - Updates for strict syntax compliancefix: BBMAP versions + Sentieon config (
6da25a0) - Remove invalid version reference, create standalone sentieon.config filestest: Update snapshots (
e806fa9)ci: Add strict syntax lint workflow (
01d18d3)docs: Fix RSEM output docs (
f79417a) - Fixstar_rsem/log/nesting, correct log file patternsdocs: Update CHANGELOG (
24d1d32)Side effects explained
Changes arose from: (1) removing conditional config wrappers for strict syntax, (2) updating modules to strict-syntax-compliant versions.
RSEM BAM input (
bam_input.nf.test.snap)rsem/→star_rsem/,*.transcript.bamno longer publishedif (!params.skip_alignment && ...)wrapper now applies config consistentlydocs/output.md; input BAMs no longer redundantly re-publishedfastp naming⚠️ BREAKING
*_1.fastp.fastq.gz→*_R1.fastp.fastq.gz(same for_2/_R2)RSeQC TIN naming
test.paired_end.sorted.summary.txt→test.summary.txtext.prefixfor cleaner namingModule snapshot changes (topic-based versions)
versions.ymlfiles, changing snapshot structure significantlyVersion reporting fix
python: null→python: "3.12.2"in pipeline snapshotsReferences
Depends on fix: Nextflow 25 strict syntax compliance for rnaseq modules and subworkflows modules#9688✅ MergedPR checklist
CHANGELOG.mdupdateddocs/output.mdupdated