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run_fusioncatcher back to fusioncatcher #641

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Merged
rannick merged 2 commits into from
Mar 25, 2025
Merged

run_fusioncatcher back to fusioncatcher #641

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8a7b54d
run_fusioncatcher back to fusioncatcher
rannick Mar 25, 2025
c416e1b
update changelog
rannick Mar 25, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -50,6 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fix error message when parameter outdir is missing [#611](https://github.com/nf-core/rnafusion/pull/611)
- Updated documentation for fusion-report score calculation to reflect 80/20 weight distribution between tool detection and database hits [#620](https://github.com/nf-core/rnafusion/pull/620)
- Update htslib and samtools version in `star/align` to 1.21 [#634](https://github.com/nf-core/rnafusion/pull/634)
- `--run_fusioncatcher` back to `fusioncatcher` [#641](https://github.com/nf-core/rnafusion/pull/641)

### Fixed

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6 changes: 3 additions & 3 deletions subworkflows/local/fusioncatcher_workflow/main.nf
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Expand Up @@ -3,13 +3,13 @@ include { FUSIONCATCHER_DETECT } from '../../../modules/local/fusioncatcher/dete
// TODO: Remove fusioncatcher_fusions as parameter.
// TODO: remove dummy file. Work with Channel.empty()
// TODO: if the files were already produced and the user want to skip the module because of this, they should be taken them from the sample sheet
// TODO: harmonize `run_fusioncatcher` and `fusioncatcher_only` parameters at main workflow level to activate/skip this one.
// TODO: harmonize `fusioncatcher` and `fusioncatcher_only` parameters at main workflow level to activate/skip this one.

workflow FUSIONCATCHER_WORKFLOW {
take:
reads // channel [ meta, [ fastqs ] ]
fusioncatcher_ref // channel [ meta, path ]
run_fusioncatcher // boolean
fusioncatcher // boolean
all // boolean
fusioninspector_only // boolean
fusioncatcher_fusions // path, string
Expand All @@ -18,7 +18,7 @@ workflow FUSIONCATCHER_WORKFLOW {
ch_versions = Channel.empty()
ch_dummy_file = file("$baseDir/assets/dummy_file_fusioncatcher.txt", checkIfExists: true)

if (( run_fusioncatcher || all) && !fusioninspector_only ) {
if (( fusioncatcher || all) && !fusioninspector_only ) {
if (fusioncatcher_fusions){

ch_fusioncatcher_fusions = reads.combine(Channel.value(file(fusioncatcher_fusions, checkIfExists:true)))
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2 changes: 1 addition & 1 deletion workflows/rnafusion.nf
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Expand Up @@ -122,7 +122,7 @@ workflow RNAFUSION {
FUSIONCATCHER_WORKFLOW (
ch_reads,
BUILD_REFERENCES.out.ch_fusioncatcher_ref, // channel [ meta, path ]
params.run_fusioncatcher,
params.fusioncatcher,
params.all,
params.fusioninspector_only,
params.fusioncatcher_fusions
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