Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

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

Merged
merged 5 commits into from
Jan 26, 2024
Merged

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

merged 5 commits into from
Jan 26, 2024

Conversation

maxibor
Copy link
Member

@maxibor maxibor commented Dec 5, 2023 •
edited
Loading

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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Dec 5, 2023 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3a65193

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

❗ 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
Merged
5 tasks
jfy133
jfy133 approved these changes Jan 26, 2024
View reviewed changes
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
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Do any of the res tof these files also need a meta? e.g. the names? Or are they not used for anything else?

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

workflows/mag.nf Show resolved Hide resolved
workflows/mag.nf Show resolved Hide resolved
subworkflows/local/gtdbtk.nf Outdated Show resolved Hide resolved
subworkflows/local/gtdbtk.nf Outdated Show resolved Hide resolved
maxibor
maxibor commented Jan 26, 2024
View reviewed changes
Copy link
Member Author

@maxibor maxibor left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

@jfy133
Copy link
Member

jfy133 commented Jan 26, 2024

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

@jfy133
Copy link
Member

jfy133 commented Jan 26, 2024

@nf-core-bot fix linting

This was referenced Jan 26, 2024
Closed
Merged
@jfy133 jfy133 merged commit 13212ab into nf-core:dev Jan 26, 2024
14 of 15 checks passed
@jfy133
Copy link
Member

jfy133 commented Jan 26, 2024

Thanks @maxibor !!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jfy133 jfy133 jfy133 approved these changes

@prototaxites prototaxites Awaiting requested review from prototaxites

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@maxibor @jfy133