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Apply the seventh set of reviewer recommendations #72

Merged
merged 9 commits into from
Aug 1, 2024
Merged

Apply the seventh set of reviewer recommendations #72

merged 9 commits into from
Aug 1, 2024

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scwatts
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@scwatts scwatts commented Jul 31, 2024

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@scwatts scwatts requested a review from seedgeorge July 31, 2024 06:13
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github-actions bot commented Jul 31, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f876e18

+| ✅ 177 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_virusbreakenddb_path not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-31 09:24:53

@scwatts scwatts mentioned this pull request Jul 31, 2024
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scwatts commented Jul 31, 2024

Force pushing latest commit to attempt to cleanly retrigger CI

@scwatts scwatts force-pushed the initial-release-review-changes branch from b994eb4 to a33f81b Compare July 31, 2024 08:39
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scwatts commented Jul 31, 2024

CI is giving the following error:

ERROR ~ mapping values are not allowed here
 in 'reader', line 2, column 109:
     ... bd13032d9db48ac3fb9e/.command.sh: line 4: samtools: command not  ... 
                                         ^


 -- Check script './subworkflows/local/utils_nfcore_oncoanalyser_pipeline/../../nf-core/utils_nfcore_pipeline/main.nf' at line: 106 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[nf-core/oncoanalyser] Pipeline completed with errors-

But I can't replicate locally. I'm going to roll back some changes to see if I can isolate the problem.

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scwatts commented Jul 31, 2024

CI appears to be having issues with a non-stub samplesheet. Adding relevant samplesheet to nf-core/test-datasets and adjust test_stub profile accordingly here. Also force pushing to clean up git history.

@scwatts scwatts mentioned this pull request Jul 31, 2024
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@scwatts scwatts force-pushed the initial-release-review-changes branch from b58a7d8 to 71e927e Compare July 31, 2024 09:12
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scwatts commented Jul 31, 2024

Another force push incoming to exclude irrelevant git history

@scwatts scwatts force-pushed the initial-release-review-changes branch from 71e927e to f876e18 Compare July 31, 2024 09:23
@scwatts scwatts requested a review from charlesshale July 31, 2024 23:03
@scwatts scwatts merged commit 41010dd into dev Aug 1, 2024
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@scwatts scwatts deleted the initial-release-review-changes branch August 1, 2024 03:52
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@charlesshale charlesshale charlesshale approved these changes

@seedgeorge seedgeorge Awaiting requested review from seedgeorge

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@scwatts @charlesshale