8000 1.1 Release by chris-cheshire · Pull Request #77 · nf-core/cutandrun · GitHub
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1.1 Release #77

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Merged
merged 149 commits into from
Jan 20, 2022
Merged

1.1 Release #77

merged 149 commits into from
Jan 20, 2022

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chris-cheshire
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@chris-cheshire chris-cheshire commented Jan 4, 2022 •
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Enhancements & fixes

  • Updated pipeline template to nf-core/tools 2.2
  • [#71] - Bumped Nextflow version 21.04.0 -> 21.10.3
  • Added pipeline diagram to [README]
  • Upgraded all modules (local and nf-core) to support the new versioning system
  • The module getchromsizes was submitted to nf-core and moved from local to nf-core
  • Added support for GFF files in IGV session generation
  • [#57, #66] - Upgraded version reporting in multiqc to support both software version by module and unique software versions. This improves detection of multi-version software usage in the pipeline
  • [#54] - Fixed pipeline error where dots in sample ids inside the sample sheet were not correctly handled
  • [#75] - Fixed error caused by emtpy peak files being passed to the CALCULATE_FRIP and CALCULATE_PEAK_REPROD python reporting modules
  • [#83] - Fixed error in violin chart generation with cast to int64

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency Old version New version
samtools 1.13 1.14

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

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/cutandrun 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).
  • 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).

Tamara Hodgetts and others added 30 commits October 21, 2021 16:16
changes made by updating all nf-core modules
78cee81
changed versioning of calculate_frip module
10000
f86e283
changed versioning of calculate_peak_reprod module
3e45a8a
updated all nf-core modules
fd347ac
Included functions, main and meta file for gunzip module
e9996f3
changed versioning of samtools_customview module
b973d10
cleaned custom view spacing
adc2d8c
changed versioning of trimgalore module
19c3cbf
changed versioning of awk_script module
e2e17d2
changed versioning of awk.nf module
35f334c
changed versioning of bedtools_genomecov_scale module
5105270
Changed versioning of generate_reports module
416cd31
Changed versioning get_chrom_sizes module
064a6fa
Merge branch 'dev' into module_versioning
5f7fc21
changed versioning igv.session module
9d8099d
changed versioning plot_consensus_peaks module
caafbc9
Added new versioning to samplesheet_check file
9439915
removed get_software_versions
931a8c9
Added CUSTOM_DUMPSOFTWAREVERSIONS module
f816bdc
Commented out all uses of get_software_versions module in cutandrun.nf
2122634
Included custom_dumpsoftwareversions & changed spacing in cutandrun.nf
d9414aa
changed dump_softwareversions module parameters import specification
4198c1b
Changed include statement for CUSTOM_DUMPSOFTWAREVERSIONS & spacing
3a3eb5f
Included CUSTOM_DUMPSOFTWAREVERSIONS call, removed get_software_versions
6ffe5f6
Included CUSTOM_DUMPSOFTWAREVERSIONS output in multiqc call
91c2291
Debugging
7980700
@chris-cheshire
test
78d3436
@chris-cheshire
tidy up
1a0e0e1
@chris-cheshire
added version to samplesheet check
fa31dcd
@chris-cheshire
remove debug
9b05619
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github-actions bot commented Jan 4, 2022

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c8c9908

+| ✅ 139 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
    • 8000
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-01-04 21:24:36

@nf-core nf-core deleted a comment from github-actions bot Jan 5, 2022
@chris-cheshire chris-cheshire added the enhancement Improvement for existing functionality label Jan 5, 2022
mashehu
mashehu approved these changes Jan 5, 2022
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Looks good to me. A bit of cleanup needed for some remnants of the old file structure for the modules, but a nf-core modules update should do the trick 🙂

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mashehu commented Jan 6, 2022

Oh another thing I saw when running the test: a rogue cut directory with h3k27me3_R1.repro.cut.bed inside is also generated in the results directory, which shouldn't be there I guess...

FriederikeHanssen
FriederikeHanssen reviewed Jan 20, 2022
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Looks good, just that the new syntax without the functions.nf and without the addParams functionality is not part of this release. I am not sure what the consensus here is about switching now or leaving it here as is, since it is quite a big change.

@FriederikeHanssen FriederikeHanssen self-requested a review January 20, 2022 09:20
FriederikeHanssen
FriederikeHanssen approved these changes Jan 20, 2022
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🚀 LGTM

@chris-cheshire chris-cheshire merged commit c30a37f into master Jan 20, 2022
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@mashehu mashehu mashehu approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@jfy133 jfy133 Awaiting requested review from jfy133

@ewels ewels Awaiting requested review from ewels

@drpatelh drpatelh Awaiting requested review from drpatelh

@maxulysse maxulysse Awaiting requested review from maxulysse

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