Enhanced BLAST results filtering #434
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Joon-Klaps
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Jun 13, 2024
CHANGELOG.md
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| @@ -36,6 +38,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements | |||
| | | `--freyja_lineages` | | |||
| | | `--skip_freyja_boot` | | |||
| | | `--additional_annotation` | | |||
| | | `--min_contig_length` | | |||
| | | `--min_perc_cgaligned` | | |||
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I'm not certain this variable is very descriptive. What about --min_perc_contig_aligned or --blast_perc_aligned or something else?
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I named it this way because the column is %cgAligned. But I can name it other way.
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In my opinion, the %cgAligned will call for questions if you see this for the first time.
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mmmm I think I'll go with --min_perc_contig_aligned and write a more exhaustive description of the BLAST headers in the documentation. The %cgAligned column has always been there, but I think it is not properly described. Thanks!
| publishDir = [ | ||
| path: { "${params.outdir}/assembly/spades/${params.spades_mode}/blastn" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| enabled: false |
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It might not always be interesting to not publish this? What about an additional variable that controls this --save_blast_unfiltered ?
If you agree make sure to keep ${meta.id}.filter.blastn
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Unfiltered blast is always saved, but it does it in the other process, here is only unfiltered blast with no header.
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It is generated inside modules/local/filter_blastn.nf
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Aaah sorry! I missed those 2 new lines :D
Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
Joon-Klaps
reviewed
Jun 13, 2024
Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
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Fixed issue #378:
.filter.blastn.txtPR checklist
nf-core lint).nextflow run . -profile 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).