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Zip ampcombi #243

Merged
merged 7 commits into from
Mar 20, 2023
Merged

Zip ampcombi #243

merged 7 commits into from
Mar 20, 2023

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louperelo
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The concatenated complete summary of all samples by AMPcombi may be very large and now is saved in a compressed file in the output directory.
(There were names missing in the manifest part of the nextflow.config, so I added them here too)

Closes issue #236

PR checklist

  • [ x] 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/funcscan 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.
  • [x ] Output Documentation in docs/output.md is updated.
  • [x ] CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@louperelo louperelo self-assigned this Mar 9, 2023
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github-actions bot commented Mar 9, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8995705

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-09 15:22:22

@louperelo
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@nf-core-bot fix linting

@Darcy220606 Darcy220606 linked an issue Mar 10, 2023 that may be closed by this pull request
Very large AMPcombi TSV files #236
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jfy133
jfy133 approved these changes Mar 17, 2023
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conf/modules.config
@@ -454,6 +454,14 @@ process {
ext.args = "--tooldict '${ext.tooldict}' --cutoff ${params.amp_ampcombi_cutoff}"
}

withName: TABIX_BGZIP {
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Needs a pattern?

@louperelo louperelo merged commit 225d501 into nf-core:dev Mar 20, 2023
@louperelo louperelo deleted the zip_ampcombi branch March 20, 2023 10:21
@jasmezz jasmezz mentioned this pull request Apr 26, 2023
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@jfy133 jfy133 jfy133 approved these changes

@jasmezz jasmezz Awaiting requested review from jasmezz

@Darcy220606 Darcy220606 Awaiting requested review from Darcy220606

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Very large AMPcombi TSV files
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@louperelo @jfy133