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Consider allowing annotation to run even if downstream screening not run #392

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jfy133 opened this issue Jul 3, 2024 · 0 comments · Fixed by #393
Open

Consider allowing annotation to run even if downstream screening not run #392

jfy133 opened this issue Jul 3, 2024 · 0 comments · Fixed by #393
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enhancement Improvement for existing functionality

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@jfy133
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jfy133 commented Jul 3, 2024

Description of feature

A few times now users have been confused that annotation files did not execute, when they did not turn on any screening workflow.

It seems sometimes people want a pipeline just to run prodigal/prokka etc.

We could change the current scheme so it always runs (or ad a validation check that if any of the downstream screening turned on, and annotation is off, it will not run). This maybe would allow us to remove this montrousity

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

        ch_new_annotation = ch_input_for_annotation
                                .join( ANNOTATION.out.faa )
                                .join( ANNOTATION.out.gbk )

    } else {
        ch_new_annotation = Channel.empty()
    }
    
@jfy133 jfy133 added the enhancement Improvement for existing functionality label Jul 3, 2024
@jfy133 jfy133 mentioned this issue Jul 3, 2024
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@jasmezz jasmezz mentioned this issue Jul 29, 2024
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