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Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
Co-authored-by: Karthik Nair <35717861+KarNair@users.noreply.github.com>
Input workflow
Issue with the previous implementation was that sometimes MULTIQC_PER_LANE would execute before the extra files were collected into `ch_multiqc_extra_files`, causing `null` to be added to the list of files passed to multiqc.
Important! Template update for nf-core/tools v2.14.1
…uts w. empty channels
Some additions
Co-authored-by: Matthias Zepper <MatthiasZepper@users.noreply.github.com>
Implement tagging system
Manual merge nf-core-tools 3.0.2
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MatthiasZepper
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Oct 29, 2024
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Thank you for the contribution and working on this task!
Unfortunately, I am missing any configuration for this module. This is highly relevant for two reasons:
1.) The publishDir directive: Initially, we had decided that Seqinspector would only inspect reads, but not alter them in any way (e.g. perform adapter-trimming) However, I agree that it is convenient to be able to perform some basic error correction and optimization in the process as well. Therefore, I support the addition of such a step, but you need to publish the resulting files so they are available later in the output directory.
2.) Currently, there are no arguments defined for the tool. Particularly for tools from the BBMap Suite, the sheer amount of settings can be overwhelming, but the arguments are also very useful for advanced customization. Please read through the description of arguments and propose some decent defaults. Hint: Consider predominantly k, subs, lowcomplexity and reorder. If you would like to enable deduplication (dedupe=t) as well, choices for dupedist, scanlimit, spantiles, adjacent and optical must be made.
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added clumpify module to the pipeline.
not sure if any of its outputs goes into multiqc (other than version).
PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).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).