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Strict-syntax compliance: Nextflow 25.10.4, nf-schema 2.6.1 #1680
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eeae227
chore: Update nf-schema to 2.6.1 for strict syntax compatibility
pinin4fjords 3c5ef8e
docs: Update CHANGELOG for nf-schema update
pinin4fjords 4db4ce4
Merge remote-tracking branch 'origin/dev' into pr-1680
pinin4fjords e2277a9
chore: bump Nextflow floor to 25.10.4 and silence strict-syntax warnings
pinin4fjords 2762439
docs(changelog): condense #1680 entry and reorder by PR number
pinin4fjords a4abbe8
chore(modules): resync 6 nf-core components to upstream master
pinin4fjords 78d3fca
docs(local-modules): add missing meta.yml for deseq2_qc and preproces…
pinin4fjords 8438147
style(local-modules): apply prettier to deseq2_qc meta.yml
pinin4fjords 802f166
docs(changelog): expand #1680 entry to cover all touched surfaces
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,149 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "deseq2_qc" | ||
| description: | | ||
| DESeq2-based sample QC: build a DESeq2 dataset from a gene-level count matrix and emit | ||
| PCA value tables, sample-distance matrices, the corresponding diagnostic PDFs and RData | ||
| objects, and the gene-level size factors. The PCA and clustering outputs are also | ||
| re-emitted as MultiQC-compatible TSVs (header prepended, file/heading labels rewritten | ||
| from a caller-supplied `args2` label so reports stay disambiguated per quantification | ||
| source - e.g. `star_salmon` vs `salmon`). | ||
| keywords: | ||
| - deseq2 | ||
| - qc | ||
| - pca | ||
| - clustering | ||
| - rnaseq | ||
| tools: | ||
| - "r-base": | ||
| description: "Base R distribution" | ||
| homepage: "https://www.r-project.org/" | ||
| documentation: "https://www.r-project.org/other-docs.html" | ||
| licence: | ||
| - "GPL v2" | ||
| identifier: "" | ||
| - "bioconductor-deseq2": | ||
| description: "Differential gene expression analysis based on the negative binomial distribution" | ||
| homepage: "https://bioconductor.org/packages/DESeq2/" | ||
| documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html" | ||
| tool_dev_url: "https://github.com/thelovelab/DESeq2" | ||
| doi: "10.1186/s13059-014-0550-8" | ||
| licence: | ||
| - "LGPL v3" | ||
| identifier: "" | ||
| input: | ||
| - - counts: | ||
| type: file | ||
| description: | | ||
| Gene-level raw count matrix (samples on columns, genes on rows) - typically the | ||
| `*.gene_counts.tsv` output of the rnaseq tximport step. | ||
| pattern: "*.{tsv,txt}" | ||
| ontologies: [] | ||
| - - pca_header_multiqc: | ||
| type: file | ||
| description: | | ||
| MultiQC custom-content header file prepended to the PCA values TSV so MultiQC | ||
| renders a labelled scatter plot. | ||
| pattern: "*.txt" | ||
| ontologies: [] | ||
| - - clustering_header_multiqc: | ||
| type: file | ||
| description: | | ||
| MultiQC custom-content header file prepended to the sample-distance matrix so | ||
| MultiQC renders a labelled heatmap. | ||
| pattern: "*.txt" | ||
| ontologies: [] | ||
| output: | ||
| pdf: | ||
| - "*.pdf": | ||
| type: file | ||
| description: Diagnostic plots (PCA biplot, sample-distance heatmap, library-size barplot) | ||
| pattern: "*.pdf" | ||
| ontologies: [] | ||
| rdata: | ||
| - "*.RData": | ||
| type: file | ||
| description: Serialised DESeq2 dataset (`dds`) and intermediate R objects | ||
| pattern: "*.RData" | ||
| ontologies: [] | ||
| pca_txt: | ||
| - "*pca.vals.txt": | ||
| type: file | ||
| description: Tab-separated PCA component values per sample | ||
| pattern: "*pca.vals.txt" | ||
| ontologies: [] | ||
| pca_multiqc: | ||
| - "*pca.vals_mqc.tsv": | ||
| type: file | ||
| description: PCA values TSV pre-pended with the MultiQC custom-content header | ||
| pattern: "*pca.vals_mqc.tsv" | ||
| ontologies: [] | ||
| dists_txt: | ||
| - "*sample.dists.txt": | ||
| type: file | ||
| description: Sample-to-sample Euclidean distance matrix | ||
| pattern: "*sample.dists.txt" | ||
| ontologies: [] | ||
| dists_multiqc: | ||
| - "*sample.dists_mqc.tsv": | ||
| type: file | ||
| description: Sample-distance matrix pre-pended with the MultiQC custom-content header | ||
| pattern: "*sample.dists_mqc.tsv" | ||
| ontologies: [] | ||
| log: | ||
| - "*.log": | ||
| type: file | ||
| description: R session info / runtime log | ||
| pattern: "*.log" | ||
| ontologies: [] | ||
| size_factors: | ||
| - "size_factors": | ||
| type: directory | ||
| description: Per-sample size factors written as individual `*.size_factors.RData` files | ||
| pattern: "size_factors" | ||
| ontologies: [] | ||
| versions_r_base: | ||
| - - ${task.process}: | ||
| type: string | ||
| description: The name of the process | ||
| - r-base: | ||
| type: string | ||
| description: The name of the tool | ||
| - "Rscript -e 'cat(as.character(getRversion()))'": | ||
| type: eval | ||
| description: The expression to obtain the version of the tool | ||
| versions_deseq2: | ||
| - - ${task.process}: | ||
| type: string | ||
| description: The name of the process | ||
| - bioconductor-deseq2: | ||
| type: string | ||
| description: The name of the tool | ||
| - 'Rscript -e "library(DESeq2); cat(as.character(packageVersion(''DESeq2'')))"': | ||
| type: eval | ||
| description: The expression to obtain the version of the tool | ||
| topics: | ||
| versions: | ||
| - - ${task.process}: | ||
| type: string | ||
| description: The name of the process | ||
| - r-base: | ||
| type: string | ||
| description: The name of the tool | ||
| - "Rscript -e 'cat(as.character(getRversion()))'": | ||
| type: eval | ||
| description: The expression to obtain the version of the tool | ||
| - - ${task.process}: | ||
| type: string | ||
| description: The name of the process | ||
| - bioconductor-deseq2: | ||
| type: string | ||
| description: The name of the tool | ||
| - 'Rscript -e "library(DESeq2); cat(as.character(packageVersion(''DESeq2'')))"': | ||
| type: eval | ||
| description: The expression to obtain the version of the tool | ||
| authors: | ||
| - "@drpatelh" | ||
| - "@pinin4fjords" | ||
| maintainers: | ||
| - "@pinin4fjords" | ||
55 changes: 55 additions & 0 deletions
55
modules/local/preprocess_transcripts_fasta_gencode/meta.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "preprocess_transcripts_fasta_gencode" | ||
| description: | | ||
| Strip the pipe-separated GENCODE metadata trailing each transcript header in a | ||
| transcript FASTA, leaving only the bare transcript identifier as the sequence name. | ||
| Required to keep GENCODE transcript IDs consistent with the GTF-derived `tx2gene` | ||
| mapping consumed downstream by Salmon, Kallisto, and tximport. Transparently | ||
| decompresses `.gz` input. | ||
| keywords: | ||
| - gencode | ||
| - transcripts | ||
| - fasta | ||
| - preprocess | ||
| - rnaseq | ||
| tools: | ||
| - "sed": | ||
| description: "GNU stream editor - used only to extract the tool version reported in the topic; the actual header rewrite is done with cut(1)." | ||
| homepage: "https://www.gnu.org/software/sed/" | ||
| documentation: "https://www.gnu.org/software/sed/manual/sed.html" | ||
| licence: | ||
| - "GPL v3" | ||
| identifier: "" | ||
| input: | ||
| - - fasta: | ||
| type: file | ||
| description: | | ||
| GENCODE transcript FASTA, optionally gzipped. Each header is expected to be of the | ||
| form `>ENST...|ENSG...|...|...` where everything from the first `|` onwards is | ||
| stripped. | ||
| pattern: "*.{fa,fasta,fa.gz,fasta.gz}" | ||
| ontologies: [] | ||
| output: | ||
| fasta: | ||
| - "*.fa": | ||
| type: file | ||
| description: Transcript FASTA with pipe-suffixed header metadata removed | ||
| pattern: "*.fa" | ||
| ontologies: [] | ||
| topics: | ||
| versions: | ||
| - - ${task.process}: | ||
| type: string | ||
| description: The name of the process | ||
| - sed: | ||
| type: string | ||
| description: The name of the tool | ||
| - "sed --version 2>&1 | sed '1!d;s/^.*) //'": | ||
| type: eval | ||
| description: The expression to obtain the version of the tool | ||
| authors: | ||
| - "@drpatelh" | ||
| - "@pinin4fjords" | ||
| maintainers: | ||
| - "@pinin4fjords" |
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