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Fix/avoid-falco-to-process-empty-fastq-file #192

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wants to merge 26 commits into from
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Fix/avoid-falco-to-process-empty-fastq-file #192

wants to merge 26 commits into from

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glichtenstein
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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/demultiplex 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).

nf-core-bot and others added 26 commits February 20, 2024 15:28
@nf-core-bot
Template update for nf-core/tools version 2.13
0de445b
@nf-core-bot
Template update for nf-core/tools version 2.13.1
10a64de
@nf-core-bot
Template update for nf-core/tools version 2.14.0
c45c906
@nf-core-bot
Template update for nf-core/tools version 2.14.1
c297bf8
@k1sauce
feat: merge nf-core template v2.14.1
77854be
@k1sauce
fix: nf-core update workflows/modules and lint
d7c160e
@k1sauce
fix: prettier lint
7a49e5c
@k1sauce
fix: samplesheet input and checks
5d305f1
@k1sauce
dev
89095db
@k1sauce
fix: capture lane in meta
14b1d61
tests: update snaps
d4d41e4
@k1sauce
fix: use fromPath factory for fqtk manifest
15b5b74
@k1sauce
test
cea6226
@k1sauce
test
3b4bce2
tests: fqtk, sgdemux
c2aa81f
@k1sauce
lint
4b23be1
@k1sauce
fix: skip multiqc
9899844
test: skip tools
b4e10b0
@maxulysse
Update linting.yml
dbc2f0a 
unpin nf-core tools
@maxulysse
Update README.md
9047ef4
@maxulysse
update nf-test
d4ff9d6
@maxulysse
update snapshot
41eba23
@maxulysse
Merge pull request nf-core#186 from nf-core/nf-core-template-merge-2.…
81e26ca 
…14.1

Important! Template update for nf-core/tools v2.14.1
@Aratz
Bump version to 1.5.0dev
d40b0d9
@maxulysse
Merge pull request nf-core#178 from Aratz/dev
6a960ff 
Post-release v1.4.1
@glichtenstein
The falco process will now only execute if the 'when' extension of th…
774288d 
…e task is either null or true, and all files in the 'reads' list are larger than 20 bytes. This ensures that the process will not run on small files (less than or equal to 20 bytes), which will Error out.
@github-actions GitHub Actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @glichtenstein,

It looks like this pull-request is has been made against the glichtenstein/demultiplex master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the glichtenstein/demultiplex dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@github-actions GitHub Actions
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github-actions bot commented May 31, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 774288d

+| ✅ 181 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-31 22:30:12

@glichtenstein glichtenstein deleted the fix/avoid-falco-to-process-empty-fastq-file branch May 31, 2024 22:35
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@blajoie blajoie Awaiting requested review from blajoie blajoie will be requested when the pull request is marked ready for review blajoie is a code owner

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5 participants
@glichtenstein @nf-core-bot @k1sauce @maxulysse @Aratz