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Patch for 2.5.0 release #534

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wants to merge 6 commits into from
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Patch for 2.5.0 release #534

wants to merge 6 commits into from

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maxibor
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@maxibor maxibor commented Nov 3, 2023

This is a patch for the 2.5.0 release, adressing the following issues:

In workflow/mag.nf 55ca012

  • 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
  • refactor: renaming reads into bins in ch_input_for_quast_bins map, quast deals with bins, not reads

In subworkflows/gtdbk.nf 2805d99

  • 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/gtdbk.nf afa3ad3

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

In modules/nf-core/gtdbtk/classifywf 54e9fc4

  • fix: update GTDB-Tk module and fix moving/compressing files

In modules/local/cat.nf and modules/local/cat_summary.nf 779fa0d

  • fix: bin2classification.names.txt needs to be decompressed for .collectFile() in order to solve the input file name collision

In bin/combine_tables.py f9c4f84

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

PR checklist

  • This comment contains a description of changes (with reason).

@maxibor
fix: handle case where genomes in depth are not processed by GTDB-Tk
f9c4f84
@maxibor
fix: bin2classification.names.txt needs to be decompressed for .colle…
779fa0d 
…ctFile()
@maxibor
update/fix: GTDB-Tk module
54e9fc4
@maxibor
fix: input file name collision for MAG_DEPTHS_SUMMARY solved by conca…
afa3ad3 
…tenating files with same name in one with .collectFile()
@maxibor
fix: busco_db needs to be cast to file to call getBaseName() function…
2805d99 
…, and failOnMistmatch needs to be False to handle unrefined genomes coming through the ch_bin_metrics(depth) channel
@maxibor
- fix: centrifuge_db needs to be in if/else scope
55ca012 
- fix: collectFile in CAT_SUMMARY and QUAST_BINS_SUMMARY to avoid input file name collision
- refactor: renaming reads into bins in ch_input_for_quast_bins map, quast deals with bins, not reads
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github-actions bot commented Nov 3, 2023

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @maxibor,

It looks like this pull-request is has been made against the maxibor/mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the maxibor/mag dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented Nov 3, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 55ca012

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.0
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-03 13:57:03

@jfy133 jfy133 marked this pull request as draft November 7, 2023 09:30
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jfy133 commented Nov 7, 2023

Note: this should be integrated into dev instead

@maxibor maxibor mentioned this pull request Dec 5, 2023
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@maxibor maxibor closed this Dec 12, 2023
jfy133 added a commit that referenced this pull request Jan 26, 2024
@jfy133
Merge pull request #548 from maxibor/patch_2_5_1
13212ab 
Patch of #534 into dev for v2.5.1
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@maxibor @jfy133