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add branch in case of no fusions #388

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merged 5 commits into from Sep 4, 2023
Merged

add branch in case of no fusions #388

merged 5 commits into from Sep 4, 2023

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rannick
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@rannick rannick commented Aug 30, 2023

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/rnafusion 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 Aug 30, 2023 •
edited

nf-core lint overall result: Passed ✅

Posted for pipeline commit 72ee2ec

+| ✅ 158 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-04 11:28:16

@rannick rannick self-assigned this Aug 30, 2023
@fevac fevac requested a review from peterpru September 4, 2023 09:39
peterpru
peterpru reviewed Sep 4, 2023
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peterpru
peterpru reviewed Sep 4, 2023
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subworkflows/local/fusioninspector_workflow.nf

if (params.whitelist) {
ch_whitelist = ch_fusion_list.combine(Channel.value(file(params.whitelist, checkIfExists:true)))
ch_whitelist = ch_fusion_list.fusions.combine(Channel.value(file(params.whitelist, checkIfExists:true)))
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What happens if there are no fusions here? It creates a ch_fusion_list.no_fusions above, but the here ch_fusion_list.fusions would be NULL, then this code would essentially output ch_whitelist = null. Then CAT_CAT(ch_whitelist) should lead to a NullPointerException or a similar error, is that correct?

Then maybe we could check first whether there are fusions?

if (ch_whitelist) {
    CAT_CAT(ch_whitelist)
} else {
    // some action when there are no fusions
}

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From what I understand: in case of no fusions, ch_fusion_list.fusions and ch_whitelist do not exist and the processes are not triggered. No error is thrown.

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Ok awesome 👍

@rannick @peterpru
Update CHANGELOG.md
72ee2ec 
Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com>
@rannick rannick merged commit 4bab85b into dev Sep 4, 2023
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@rannick rannick mentioned this pull request Sep 6, 2023
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@rannick rannick deleted the fix_no_fusions branch September 22, 2023 06:49
@rannick rannick mentioned this pull request Sep 22, 2023
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