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Patch of #534 into dev for v2.5.1#548

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jfy133 merged 5 commits intonf-core:devfrom
maxibor:patch_2_5_1
Jan 26, 2024
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Patch of #534 into dev for v2.5.1#548
jfy133 merged 5 commits intonf-core:devfrom
maxibor:patch_2_5_1

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@maxibor maxibor commented Dec 5, 2023 •
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This is a patch for the 2.5.1 release, adressing the following issues (first pointed out in #534):

In workflow/mag.nf

  • fix: centrifuge_db needs to be in if/else scope
  • fix: collectFile in CAT_SUMMARY and QUAST_BINS_SUMMARY to avoid input file name collision

In subworkflows/gtdbk.nf

  • fix: busco_db needs to be cast to file to call getBaseName() function,
  • failOnMistmatch needs to be False to handle unrefined genomes coming through the ch_bin_metrics(depth) channel

In subworkflows/depths.nf

  • fix: input file name collision for MAG_DEPTHS_SUMMARY solved by concatenating files with same name in one with .collectFile()

In modules/local/cat.nf and modules/local/cat_summary.nf

  • fix: bin2classification.names.txt needs to be decompressed for .collectFile() in order to solve the input file name collision, and merging is very simplified

In bin/combine_tables.py f9c4f84

  • fix: handle case where genomes in depth files were not processed by GTDB-Tk

Would close #532 and #530

Battle tested with the following command:

nextflow run /home/maxime_borry/tmp/mag \
	-profile eva,archgen,debug \
	--input /home/maxime_borry/tmp/mag_test/samplesheet_real_data.csv \
	--outdir test_results \
	--igenomes_base "/home/maxime_borry/SDAG_old/04_genomes/" \
	--host_genome GRCh38 \
	--skip_spades \
	--skip_spadeshybrid \
	--skip_krona \
	--skip_prokka \
	--busco_auto_lineage_prok \
	--bin_domain_classification \
	--ancient_dna \
	--binning_map_mode own \
	--refine_bins_dastool \
	--postbinning_input both \
	--busco_db "/r1/people/maxime_borry/02_db/busco_downloads" \
	--run_gunc \
	--gunc_db /r1/people/maxime_borry/02_db/gunc/gunc_db_progenomes2.1.dmnd \
	--gtdb_db /home/maxime_borry/02_db/gtdb/r207/gtdbtk_r207_v2_data.tar.gz \
	--gtdbtk_min_completeness 1 \
	--gtdbtk_max_contamination 20 \
	--cat_db "/home/maxime_borry/02_db/cat/CAT_prepare_20210107/" \
	-dump-channels \
	-resume \
	-with-tower
Screenshot 2023-12-05 at 17 30 18

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions Bot commented Dec 5, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3a65193

+| ✅ 161 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-26 15:23:49

@maxibor maxibor mentioned this pull request Jan 25, 2024
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jfy133
jfy133 approved these changes Jan 26, 2024
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Comment thread modules/local/cat.nf
Comment on lines +14 to +21
tuple val(meta), path("*.bin2classification.names.txt") , emit: tax_classification_names
path("*.ORF2LCA.names.txt.gz") , emit: orf2lca_classification
path("raw/*.ORF2LCA.txt.gz") , emit: orf2lca
path("raw/*.predicted_proteins.faa.gz") , emit: faa
path("raw/*.predicted_proteins.gff.gz") , emit: gff
path("raw/*.log") , emit: log
path("raw/*.bin2classification.txt.gz") , emit: tax_classification_taxids
path "versions.yml" , emit: versions
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Do any of the res tof these files also need a meta? e.g. the names? Or are they not used for anything else?

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None of these files are re-used later, hence no meta for them.

Comment thread workflows/mag.nf
Comment thread workflows/mag.nf
Comment thread subworkflows/local/gtdbtk.nf Outdated
Comment thread subworkflows/local/gtdbtk.nf Outdated
maxibor
maxibor commented Jan 26, 2024
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Do any of the res tof these files also need a meta? e.g. the names? Or are they not used for anything else?

None of these are needed for later, hence no meta

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jfy133 commented Jan 26, 2024

We can ignore the Prettier error, it's a bug in the template rather than us.

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jfy133 commented Jan 26, 2024

@nf-core-bot fix linting

This was referenced Jan 26, 2024
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@jfy133 jfy133 merged commit 13212ab into nf-core:dev Jan 26, 2024
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jfy133 commented Jan 26, 2024

Thanks @maxibor !!

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@jfy133 jfy133 jfy133 approved these changes

@prototaxites prototaxites Awaiting requested review from prototaxites prototaxites is a code owner

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