Add a feature to generate samplesheet for differentialabundance #546
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jfy133
reviewed
Oct 15, 2024
conf/modules.config
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| pattern: '*.{tsv,csv,arrow,parquet,biom}' | ||
| ], | ||
| [ path: { "${params.outdir}/downstream_samplesheets/differentialabundance/"}, | ||
| mode: params.publish_dir_mode, |
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These should only be enabled if the --generate_samplesheet_xxxx parameters are used!
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| - `samplesheet.csv`: A samplesheet for each classifier. | ||
| - `matrix.csv`: The output from taxpasta. |
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I think you should copy here also the note beflow about hte missing conditions
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| ch_colnames = Channel.of('sample') | ||
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| channelToSamplesheet(ch_colnames, ch_list_for_samplesheet, "downstream_samplesheets/differentialabundance", "samplesheet_${samplesheet_name}" ) |
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Please see the latest function as in detaxizer! It's tweaked again (sorry about that!)
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PR checklist
nf-core 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).