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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: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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- Add bbmap/clumpify module with local multiqc_files topic patch - Add nf-test for bbmap/clumpify tool - Update CHANGELOG, CITATIONS, README, docs, schema, and config - Add Erkut Ilaslan as contributor - Configure memory and ext.args for duplication assessment
SPPearce
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Jun 12, 2026
SPPearce
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SPPearce
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What will happen with seqtk sample? Does that sample at random, or take the first N?
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| [BBMap Clumpify](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/) removes duplicates from sequencing data and creates smaller, faster gzipped FASTQ files. This is particularly useful for reducing file sizes while maintaining data quality. |
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| [BBMap Clumpify](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/) removes duplicates from sequencing data and creates smaller, faster gzipped FASTQ files. This is particularly useful for reducing file sizes while maintaining data quality. | |
| [BBMap Clumpify](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/) removes duplicates from sequencing data and creates smaller, faster gzipped FASTQ files. This is particularly useful for reducing file sizes while maintaining data quality. Please note that the resulting files will not be random, so tools that take the first X reads will return a biased sample. |
| ch_sample = sample_size ? SEQTK_SAMPLE.out.reads : ch_samplesheet | ||
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| // STEP 04: MORE QC ON FASTQ FILES (CAN BE SUMSAMPLED) |
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| // STEP 04: MORE QC ON FASTQ FILES (CAN BE SUMSAMPLED) | |
| // STEP 04: MORE QC ON FASTQ FILES (CAN BE SUBSAMPLED) |
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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).