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Release PR for 3.0.3 #656

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Release PR for 3.0.3 #656

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@jfy133 jfy133 commented Aug 22, 2024

Patch release for a variety of bugs:

  • #648 - Fix sample ID/assembly ID check failure when no IDs match (reported by @zackhenny, fix by @prototaxites)
  • #646 - GTDB-Tk directory input now creates a value channel so it runs for all entries to the process and not just the first (reported by @amizeranschi, fix by @prototaxites).
  • #639 - Fix pipeline failure when a sample produces only a single bin (fix by @d-callan)
  • #651 - Replace base container for bash only modules to reduce number of containers in pipeline (reported and fixed by @harper357)
  • #652 - Fix documentation typo in using user-defined assembly parameters (reported and fixed by @amizeranschi)
  • #653 - Fix overwriting of per-bin 'raw' GUNC RUN output files (multi-bin summary tables not affected) (reported by @zackhenny and fixed by @jfy133)

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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

jfy133 and others added 30 commits July 4, 2024 08:41
@jfy133
Post release bump
127e394
@jfy133
Merge pull request #636 from nf-core/postreleasebump
65c4fd8 
Post release version bump
@d-callan
only make bin depths plots for cases w >2 samples and >2 bins
3b95035
@prototaxites
Update gtdbtk.nf
8082972
@prototaxites
Update gtdbtk.nf
deab007
@prototaxites
Update CHANGELOG.md
5b9c4f1
@prototaxites
Fix code that combines assembly and sample IDs for checking
8f4147f
@prototaxites
Update changelog
86412f0
@jfy133
Merge pull request #646 from prototaxites/fix_gtdb_dir_input
a4adc3d 
Fix GTDB-Tk directory input
@prototaxites
Merge branch 'dev' into fix_match
3668376
@prototaxites @jfy133
Update CHANGELOG.md
f143707 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@prototaxites @jfy133
Update subworkflows/local/utils_nfcore_mag_pipeline/main.nf
098c192 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@prototaxites @jfy133
Update CHANGELOG.md
3b509ed 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
@prototaxites
Merge pull request #648 from prototaxites/fix_match
6ebc119 
Fix match check of assembly and sample IDs
@d-callan
clarify when clustered heatmaps will be produced as outputs
66a0af4
@d-callan
add bug fix 639 to changelog
f7c8aca
@nf-core-bot
[automated] Fix code linting
bd3e813
@jfy133
Merge branch 'dev' into fix-638
6445d78
@jfy133
Add @d-callan and other recent code contributors
83f1fe7
@jfy133
Add other third wave of developer leads to authors
f79135c
@nf-core-bot
[automated] Fix code linting
b708160
@jfy133
Update subworkflows/local/depths.nf
e7ebbfa
@jfy133
Update LICENSE to include more recent contributors
36cfd42
@jfy133
Merge pull request #639 from nf-core/fix-638
171ea0d 
Fix #638 [MAG_DEPTHS_PLOT fails if only a single bin is produced]
@harper357
replaced old MultiQC containers with nf-core/ubuntu:20.04
5851a1d
@jfy133
Update CHANGELOG
bd0ef3b
@amizeranschi
Update nextflow_schema.json
993ac6d 
Remove "=" sign from parameter value assignment
@amizeranschi
Merge pull request #652 from nf-core/amizeranschi-patch-1
225257b 
Update nextflow_schema.json
@jfy133
Merge pull request #651 from harper357/container_sync
6a40905 
Change unnecessary MultiQC containers to nf-core/ubuntu:20.04
@jfy133
Fix GUNC overwriting of raw output files
364b3ee
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a3c3471

+| ✅ 305 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.0.3
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-22 13:36:31

heuermh
heuermh approved these changes Aug 22, 2024
View reviewed changes
subworkflows/local/depths.nf
ch_mag_depths_plot = MAG_DEPTHS.out.depths
.map { meta, bin_depths_file ->
if (getColNo(bin_depths_file) > 2) [ meta, bin_depths_file ]
if (getColNo(bin_depths_file) > 2 && getRowNo(bin_depths_file) > 2) [ meta, bin_depths_file ]
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This appears to read bin_depths_file twice. If that file is expected to ever be large, may want to implement both column and row filters in the same method.

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@heuermh heuermh heuermh approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@jfy133 @heuermh @maxulysse @d-callan @prototaxites @nf-core-bot @harper357 @amizeranschi