Add kraken2 phylogenetic assignment subworkflow#47
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ctuni wants to merge 250 commits intonf-core:devfrom
Open
Add kraken2 phylogenetic assignment subworkflow#47ctuni wants to merge 250 commits intonf-core:devfrom
ctuni wants to merge 250 commits intonf-core:devfrom
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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
…re_than_1_fastq_file Patch fastqscreen to handle multiple input FASTQ files
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
….2.dev0 Important! Template update for nf-core/tools v3.1.2.dev0
Add skip tools parameter for tool selection
Important! Template update for nf-core/tools v3.2.0
Set up nft-utils in tests
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Added a subworkflow for a "phylogenetic QC" that does kraken2 assignment for each sample and then plots them on an interactive krona plot. I have not added the kraken2 reports to multiqc, this should be the next step.
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).