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fix grouping issues
Revert nf-cmgg/configs back to nf-core/configs
Publish multiqc data alongside the report
* update pixi env * bump picard * bump nft-utils
* update pixi env * bump picard * bump nft-utils * add resourceLimits * nf-core lint * update pixi env * bump picard * bump nft-utils * add resourceLimits * fix tests * fix nf-core lint * ro-crate * linting * drop issue template config * fix snapshots - ignore mmd files * update ngsbits
* drop fastq inputs support * drop fastq inputs support * fix linting * nf lint
* add samtools/depth * drop fastq inputs support * drop fastq inputs support * add hm conversion function * fix linting * nf lint * drop some bwa leftovers * update dependencies * intermittent commit * make sure everything runs * Add depth filter, publish depth results, make cram compatible * Update test inputs * fix test conf * MOAR fixes * update snapshot * fix aws access in ci * implement filter func * update samtools depth * fix linting * fix syntax and outputs * update snaps * add extra test cases * drop pool count to catch excluding samples * fix gk * fix always index issue * use compressed fasta for tests, fix snapshot * fix nftignore * fix review comments * add metro map by nf-metro * Update subworkflows/local/utils_nfcmgg_sampletracking_pipeline/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update subworkflows/local/utils_nfcmgg_sampletracking_pipeline/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
* fix linting * Update subworkflows/local/utils_nfcmgg_sampletracking_pipeline/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.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: 4.1.0. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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nvnieuwk
approved these changes
Oct 26, 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).