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Fix preannotated input (BGC workflow) #394

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Jul 4, 2024
Merged

Fix preannotated input (BGC workflow) #394

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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#371](https://github.com/nf-core/funcscan/pull/371) Fixed AMRFinderPlus parameter `arg_amrfinderplus_name`. (by @m3hdad)
- [#376](https://github.com/nf-core/funcscan/pull/376) Fixed an occasional RGI process failure when certain files not produced. (❤️ to @amizeranschi for reporting, fix by @amizeranschi & @jfy133)
- [#386](https://github.com/nf-core/funcscan/pull/386) Updated DeepBGC module to fix output file names, separate annotation step for all BGC tools, add warning if no BGCs found, fix MultiQC reporting of annotation workflow. (by @jfy133, @jasmezz)
- [#392](https://github.com/nf-core/funcscan/pull/392) Fix a docker/singularity only error appearing when running with conda. (❤️ to @ewissel for reporting, fix by @jfy33 & @jasmezz)
- [#392](https://github.com/nf-core/funcscan/pull/392) Fixed a docker/singularity only error appearing when running with conda. (❤️ to @ewissel for reporting, fix by @jfy33 & @jasmezz)
- [#394](https://github.com/nf-core/funcscan/pull/394) Fixed BGC input channel: pre-annotated input is picked up correctly now. (by @jfy133, @jasmezz)

### `Dependencies`

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8 changes: 4 additions & 4 deletions workflows/funcscan.nf
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Expand Up @@ -135,9 +135,9 @@ workflow FUNCSCAN {
}

// Mix back the preannotated samples with the newly annotated ones
ch_prepped_input = ch_intermediate_input.preannotated
.mix( ch_new_annotation )
ch_prepped_input = ch_new_annotation
.filter { meta, fasta, faa, gbk -> meta.category != 'long' }
.mix( ch_intermediate_input.preannotated )
.multiMap {
meta, fasta, faa, gbk ->
fastas: [meta, fasta]
Expand All @@ -147,9 +147,9 @@ workflow FUNCSCAN {

if ( params.run_bgc_screening ){

ch_prepped_input_long = ch_intermediate_input.preannotated
.mix( ch_new_annotation )
ch_prepped_input_long = ch_new_annotation
.filter { meta, fasta, faa, gbk -> meta.category == 'long'}
.mix( ch_intermediate_input.preannotated )
.multiMap {
meta, fasta, faa, gbk ->
fastas: [meta, fasta]
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