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Update main.nf #203

Merged
merged 3 commits into from
Jun 26, 2022
Merged

Update main.nf #203

merged 3 commits into from
Jun 26, 2022

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ypriverol
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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/quantms 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).

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github-actions bot commented Jun 26, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit b043721

+| ✅ 146 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-26 07:55:05

@ypriverol
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@daichengxin in the pmultiqc, the pipeline is expecting an sdrf like

if 'quantms/sdrf' not in config.sp:
        config.update_dict(config.sp, {'quantms/sdrf': {'fn': '*.sdrf.tsv', 'num_lines': 0}, 'shared': False})

line: https://github.com/bigbio/pmultiqc/blob/296faaa71aea4563cb89442314b7ee99578b5b57/pmultiqc/main.py#L36

However, the log file, the sdrf looks like ./results/PXD026600.sdrf_openms_design.tsv.

Probably it will not be picked.

@daichengxin
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daichengxin commented Jun 26, 2022 •
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The experimental design file can also be captured. Because the user does not necessarily pass in sdrf. @ypriverol And pattern can be modified by yaml file. https://github.com/bigbio/quantms/blob/dev/assets/multiqc_config.yml

@ypriverol ypriverol merged commit d6e3f37 into dev Jun 26, 2022
@ypriverol ypriverol deleted the patch-pmultiqc-0.0.12 branch November 3, 2023 09:25
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@ypriverol @daichengxin