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Add kraken2 phylogenetic assignment subworkflow #47
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Original file line number | Diff line number | Diff line change |
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@@ -26,6 +26,40 @@ process { | |
ext.args = '--quiet' | ||
} | ||
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withName: 'KRAKEN2_KRAKEN2' { | ||
publishDir = [ | ||
path: { "${params.outdir}/kraken2_reports" }, | ||
mode: params.publish_dir_mode, | ||
saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
] | ||
} | ||
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withName: 'KRONA_KTUPDATETAXONOMY' { | ||
publishDir = [ | ||
path: { "${params.outdir}/kraken2_reports/krona_reports" }, | ||
mode: params.publish_dir_mode, | ||
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
enabled: false | ||
] | ||
} | ||
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withName: 'KRONA_KTIMPORTTAXONOMY' { | ||
publishDir = [ | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. same as before |
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path: { "${params.outdir}/kraken2_reports/krona_reports" }, | ||
mode: params.publish_dir_mode, | ||
saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
] | ||
} | ||
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withName: 'UNTAR' { | ||
publishDir = [ | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. I'm not sure you want to output the kraken db, because it's size can be huge (depending on the selected one) and also it has been previously downloaded by the user, so already in user's device? You may want to use the storeDir in case you want to store the db and reuse it for later without the need of publishing it in the output There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. I see what you mean! I could create a patch to the UNTAR module to add the storeDir directive, that would also need some changes to the config but it can be done. In any case, to avoid unnecessary waste of space by saving the uncompressed database, the pipeline works differently if the user provides a gzipped database or an uncompressed one. If the pipeline is gzipped, the The outputting of the uncompressed kraken2 db is turned off by default by the If the database is uncompressed, and the user passes a path to the |
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path: { "${params.outdir}/kraken2_db" }, | ||
mode: params.publish_dir_mode, | ||
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
enabled: params.save_uncompressed_k2db | ||
] | ||
} | ||
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withName: 'MULTIQC_GLOBAL' { | ||
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } | ||
publishDir = [ | ||
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I think there is a general statement for this in this (file)[https://github.com/nf-core/seqinspector/blob/31c1f829d97c4b98d21b68beed4af050fd331a37/conf/modules.config#L15], so I don't think is needed to add it twice, except if that bit is going to be removed it later?
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There is! I just added it here for two reasons: the first is that I wanted more descriptive names for the folders (
kraken2_reports
instead of justkraken2
) and I wanted the krona plots to be inside thekraken2_reports
folder, with a more descriptive name as well.The second reason I have added this seemingly redundant code is that kraken2 and kronatools can produce more output than what is produced now. I left these lines here looking into the future: they might need to be modified depending on the needs of the pipeline once it reaches a more stable status.