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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

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ca52d58
add branch in case of no fusions
rannick Aug 30, 2023
a5805ca
Merge branch 'dev' into fix_no_fusions
rannick Aug 30, 2023
9d1b32a
Merge branch 'dev' into fix_no_fusions
rannick Aug 30, 2023
6b79984
update changelog
rannick Sep 4, 2023
72ee2ec
Update CHANGELOG.md
rannick Sep 4, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380)
- Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385)
- Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386)
- The fusion lists is updated to contain to branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388)
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### Removed

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12 changes: 8 additions & 4 deletions subworkflows/local/fusioninspector_workflow.nf
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Expand Up @@ -17,19 +17,23 @@ workflow FUSIONINSPECTOR_WORKFLOW {
main:
ch_versions = Channel.empty()
index ="${params.starfusion_ref}"
ch_fusion_list = params.fusioninspector_filter ? fusion_list_filtered : fusion_list
ch_fusion_list = ( params.fusioninspector_filter ? fusion_list_filtered : fusion_list )
.branch{
no_fusions: it[1].size() == 0
fusions: it[1].size() > 0
}

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 👍

.map { meta, fusions, whitelist -> [ meta, [fusions, whitelist] ] }

CAT_CAT(ch_whitelist) // fusioninspector takes care of possible duplicates
ch_versions = ch_versions.mix(CAT_CAT.out.versions)

ch_fusion_list = CAT_CAT.out.file_out
ch_fusion_list.fusions = CAT_CAT.out.file_out
}

reads_fusion = reads.join(ch_fusion_list )
reads_fusion = reads.join(ch_fusion_list.fusions )

FUSIONINSPECTOR( reads_fusion, index)
ch_versions = ch_versions.mix(FUSIONINSPECTOR.out.versions)
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