Add chelae/trim as an alternate trimming tool#260
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Install nf-core/chelae/trim module with patch for multiqc_files topic channel on json and metrics outputs. Add as an alternative to fastp for adapter trimming and quality filtering of short-read FASTQ data. Generated by opencode
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I choose not to include a subway map update, as I have plans to refactor it, so that can go in a separate PR |
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mashehu
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| Currently the `tools` param can have the following values: bbmap_clumpify, checkqc, fastp, fastqc, fastqe, fastqscreen, fq_lint, kraken2, multiqcsav, picard_collecthsmetrics, picard_collectmultiplemetrics, riker, rundirparser, seqkit_stats, seqfu_stats, sequali and toulligqc. | ||
| Currently the `tools` param can have the following values: bbmap_clumpify, checkqc, chelae, fastp, fastqc, fastqe, fastqscreen, fq_lint, kraken2, multiqcsav, picard_collecthsmetrics, picard_collectmultiplemetrics, riker, rundirparser, seqkit_stats, seqfu_stats, sequali and toulligqc. |
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if only we had a place where this is updated automatically... 😉
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Waiting on the following PR for minor code polish:
Add chelae/trim from nf-core/modules as an alternative to fastp for adapter trimming and quality filtering of short-read FASTQ data.
Changes
nf-core/chelae/trimmodule with patch formultiqc_filestopic channel on json and metrics outputsCHELAE_TRIMinclude, invocation (gated by--tools chelae), andchelae_readsworkflow outputnextflow_schema.jsonpatterns fortools,skip_tools, andsubsample_toolschelaetoallbundle andtoolReferencesMap()Checklist
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Verified by @maxulysse