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Fix tool execution if annotation workflow is skipped #406

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Jul 23, 2024
Merged

Fix tool execution if annotation workflow is skipped #406

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#391](https://github.com/nf-core/funcscan/pull/391) Made all "database" parameter names consistent. (by @jasmezz)
- [#397](https://github.com/nf-core/funcscan/pull/397) Removed deprecated AMPcombi module, fixed variable name in BGC workflow, updated minor parts in docs (usage, parameter schema). (by @jasmezz)
- [#402](https://github.com/nf-core/funcscan/pull/402) Fixed BGC length calculation for antiSMASH hits by comBGC. (by @jasmezz)
- [#406](https://github.com/nf-core/funcscan/pull/406) Fixed prediction tools not being executed if annotation workflow skipped. (by @jasmezz)

### `Dependencies`

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4 changes: 2 additions & 2 deletions workflows/funcscan.nf
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Expand Up @@ -122,7 +122,7 @@ workflow FUNCSCAN {
*/

// Some tools require annotated FASTAs
if ( ( params.run_arg_screening && !params.arg_skip_deeparg ) || ( params.run_amp_screening && ( params.amp_run_hmmsearch || !params.amp_skip_amplify || !params.amp_skip_ampir ) ) || ( params.run_bgc_screening ) ) {
if ( ( params.run_arg_screening && !params.arg_skip_deeparg ) || ( params.run_amp_screening ) || ( params.run_bgc_screening ) ) {
ANNOTATION( ch_input_for_annotation )
ch_versions = ch_versions.mix( ANNOTATION.out.versions )

Expand All @@ -131,7 +131,7 @@ workflow FUNCSCAN {
.join( ANNOTATION.out.gbk )

} else {
ch_new_annotation = Channel.empty()
ch_new_annotation = ch_intermediate_input.fastas
}

// Mix back the preannotated samples with the newly annotated ones
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