chore: update all modules and subworkflows to latest#194
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Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- nfschema plugin: pass cli_typecast (10th input) - samtools/view: add region BED input in coverage_tracks - bam_sort ecosystem: bai->index output rename (STAR, dedup subworkflows) - fastq_align_star / bam_dedup_umi: bundle fasta+fai inputs; drop bam_csi_index - quantify_pseudo_alignment: pass skip_merge; drop topic-migrated versions - anota2seqrun: drop topic-migrated versions mix [skip ci] Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
fastq_qc_trim_filter_setstrandedness now emits multiqc_files as [meta, file] tuples; strip meta at the call site so the downstream flatten/collect does not leak the meta map into MultiQC path inputs. [skip ci] Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
nf-schema 2.7.x coerces CLI string values to their schema-declared types during validation, fixing boolean CLI flags (e.g. --extended_orf_analysis true) failing under the Nextflow 26.x strict syntax parser. Matches the cli_typecast input on the updated utils_nfschema_plugin subworkflow. [skip ci] Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
nf-schema 2.7.2 requires Nextflow >=25.10.0; bump the manifest floor, CI matrix, and README badge accordingly. [skip ci] Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
ch_fasta.combine(ch_fai) yields a queue channel; without .first() the genome/transcriptome BAM_SORT_STATS reference is consumed by the first sample only, starving all others. Restore .first() so the reference is reused across every sample. [skip ci] Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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The updated bowtie2/align module snapshot contains a FASTQ quality string with '<<<<<<<<' (a valid Illumina quality run), which the merge_markers lint test flags as a conflict marker.
…apshots The updated toolchain produces trimmed/filtered reads in a non-deterministic order, so FastQC's order-sensitive sequence duplication estimates (and the per-run MultiQC fastqc data files) vary run to run. Exclude them via .nftignore alongside the existing top_overrepresented exclusion, and drop the corresponding entries from the pipeline snapshots.
The updated seqkit stats output changes the ribo_sample.tsv checksum.
Update dotseq/dotseq (nf-core/modules#12230) so plotDOT() actually emits the heatmap PNG, and pass --orf_type_main_value canonical_cds so the heatmap pairs against riboseq's main-ORF label.
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Description
Release-preparation update that brings every nf-core
modules/andsubworkflows/component up to its latest revision (via nf-core/tools 4.0.2) and reconciles the pipeline with the interface changes those updates introduce. Scope is deliberately limited to component updates and the wiring needed to accommodate them; no pipeline template sync.Components updated
masterrevisions (nf-core modules update --all,nf-core subworkflows update --all).Interface reconciliation
The component bump carried breaking interface changes, accommodated in the local workflow/subworkflows:
baioutput is renamed toindex(propagated through the STAR alignment and UMI-dedup subworkflow call sites);samtools/viewgained a region-BED input, added in the coverage-tracks subworkflow.fastq_align_starandbam_dedup_uminow take[meta, fasta, fai]tuples. Reference channels are built as value channels (.first()) so the per-sampleBAM_SORT_STATS_SAMTOOLSreference is reused across all samples.skip_mergeinput.cli_typecastinput.versions.ymlpath outputs to theversionstopic channel; the now-removed.out.versionsemits are dropped where the topic channel already collects them (anota2seqrun, the quantify subworkflows), and the QC subworkflow'smultiqc_files(now[meta, file]tuples) has its meta stripped before the MultiQC file collection.Dependencies
Testing
All 11 pipeline nf-test snapshots regenerated on x86_64 under Nextflow 25.10.0 with nf-test 0.9.3, matching CI.
🤖 Generated with Claude Code