Nextclade Subworkflow #28
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BioWilko
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BioWilko
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Seems like a good start for nextclade support but I think it needs to be integrated into the pipeline a bit better before we can merge, specifically I think nextclade results need to be nicely included in the run / sample reports when run.
The docs also need to make it very clear that the nextclade functionality doesn't support multi virus runs / multi pathogen schemes
| - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. | ||
| - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. | ||
| - Parameters used by the pipeline run: `params.json`. | ||
| - Clade/Lineages are output as a tsv: `lineages.tsv` |
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This should have its own section with more details
modules/local/generate_run_report/templates/generate_run_report.py
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Thanks Sam for the feedback, apologies for some of those changes. It was a bad merge on my end. I'll work on making the changes. |
Revamp nextclade subworkflow, changes
HTML output
Better handling of optional inputs for GENERATE_RUN_REPORT
Moved nextclade into amplicon-nf
Capture nextclade
Removed up unused params
* chore: format imports correctly
* chore: remove channel for nextclade tag
* chore: rename module
* chore: rename subworkflow
* add lineage tab into the sample run report
* chore: first attempt implement html output for nextclade
* chore: add nextclade table to template
* chore: add nextclade for file renaming
* chore: rename nextclade tags to be simple
* chore: simplify nextclade data parsing into payload
* chore: WORK IN PROGRESS - adding optional nextclade channel
* chore: move nextclade workflow into amplicon-nf.nf
* add nextclade tsv to inputs
* chore: simplify code
* chore: first working version of new nextclade workflow
* chore: added NO_FILE to handle optional input
* feat: nextclade html output
* chore: simplify run report code
* chore: remove unused param
* chore: remove nextclade settings; tsv output not produced
* chore: remove fasta_header_extra param
* chore: output software version
* chore: capture nextclade version
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Co-authored-by: Josh Zhang <zjs0317@gmail.com>
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I've pushed a bunch of code and improvements. I haven't updated the documentation, something I'm going to ping you on slack to discuss where I should add more information. |
| from jinja2 import Environment, FileSystemLoader, select_autoescape | ||
| from primalbedtools.amplicons import create_amplicons | ||
| from primalbedtools.bedfiles import BedLine | ||
| from primalbedtools.scheme import Scheme |
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Unfortunately I had linter (ruff) on when working on this python script, so it moved a bunch of the imports around. It also changed some quotations from double to singular. Hope that's okay?
| [meta, bed, depth_tsvs, amp_depth_tsvs, coverage_tsvs, [], samplesheet_csv] | ||
| } | ||
| } | ||
| // massage optional inputs |
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I rewrote this code to to take in more inputs without an if/else statement to accommodate the optional nextclade input. However, I ran into a problem where I just couldn't get the channel to be optionally taken into the GENERATE_RUN_REPORT process. I solution I ended up with was the assets/NO_FILE trick documented here.
While the code doesn't handle nextclade input, it still better than the if else statement. I can revert if you prefer the other version.
| } | ||
| // massage optional inputs | ||
| ch_msas_opt = params.primer_mismatch_plot ? ch_msas_by_scheme : channel.empty() | ||
| ch_nextclade_opt = params.nextclade ? ch_nextclade_tsv : channel.fromPath("$projectDir/assets/NO_FILE") |
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| ch_nextclade_opt = params.nextclade ? ch_nextclade_tsv : channel.fromPath("$projectDir/assets/NO_FILE") | |
| ch_nextclade_opt = params.nextclade ? ch_nextclade_tsv : channel.empty() |
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I've seen the empty file trick before and I dislike it, seems hacky, there's ways to handle it inside nextflow.
| depth, | ||
| amp, | ||
| cov, | ||
| msas ?: [], |
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pack the nextclade TSV in here
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Implement nextclade on a per organism basis (not per sample). One issue with this PR is testing, should subworkflows require separate testing?
Please let me know what you think and if you suggest any changes.
PR checklist
nf-core pipelines lint).WARNINGS are produced for many of the pipeline files - For the new subworkflow warning is related to outputting a version, which does happen.
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.Haven't added anything to change log - it's not up to date?
README.mdis updated (including new tool citations and authors/contributors).