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Conda antismash vbug #393

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merged 3 commits into from
Jul 3, 2024
Merged

Conda antismash vbug #393

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d8bd497
Fix docker/singularity only antismash directory error when conda sele…
jfy133 Jul 3, 2024
5c772ac
Actual CHGL message
jfy133 Jul 3, 2024
cad0614
Apply suggestions from code review [skip ci]
jasmezz Jul 3, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -28,6 +28,7 @@ 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)

### `Dependencies`

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11 changes: 7 additions & 4 deletions subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
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Expand Up @@ -139,20 +139,23 @@ workflow PIPELINE_COMPLETION {
// Check and validate pipeline parameters
//
def validateInputParameters() {
// Validate antiSMASH inputs
// Validate antiSMASH inputs for containers
// 1. Make sure that either both or none of the antiSMASH directories are supplied
if ( ( params.run_bgc_screening && !params.bgc_antismash_databases && params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash) || ( params.run_bgc_screening && params.bgc_antismash_databases && !params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash ) ) error("[nf-core/funcscan] ERROR: You supplied either the antiSMASH database or its installation directory, but not both. Please either supply both directories or none (letting the pipeline download them instead).")
if ( ['docker', 'singularity'].contains(workflow.containerEngine) && (( params.run_bgc_screening && !params.bgc_antismash_databases && params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash) || ( params.run_bgc_screening && params.bgc_antismash_databases && !params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash )) )
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error("[nf-core/funcscan] ERROR: You supplied either the antiSMASH database or its installation directory, but not both. Please either supply both directories or none (letting the pipeline download them instead).")

// 2. If both are supplied: Exit if we have a name collision error
else if ( params.run_bgc_screening && params.bgc_antismash_databases && params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash ) {
else if ( ['docker', 'singularity'].contains(workflow.containerEngine) && ( params.run_bgc_screening && params.bgc_antismash_databases && params.bgc_antismash_installationdirectory && !params.bgc_skip_antismash ) ) {
antismash_database_dir = new File(params.bgc_antismash_databases)
antismash_install_dir = new File(params.bgc_antismash_installationdirectory)
if ( antismash_database_dir.name == antismash_install_dir.name ) error("[nf-core/funcscan] ERROR: Your supplied antiSMASH database and installation directories have identical names: \"" + antismash_install_dir.name + "\".\nPlease make sure to name them differently, for example:\n - Database directory: "+ antismash_database_dir.parent + "/antismash_db\n - Installation directory: " + antismash_install_dir.parent + "/antismash_dir")
}

// 3. Give warning if not using container system assuming conda

if ( params.run_bgc_screening && ( !params.bgc_antismash_databases || !params.bgc_antismash_installationdirectory ) && !params.bgc_skip_antismash && ( session.config.conda && session.config.conda.enabled ) ) { log.warn "[nf-core/funcscan] Running antiSMASH download database module, and detected conda has been enabled. Assuming using conda for pipeline run. Check config if this is not expected!" }
if ( params.run_bgc_screening && ( !params.bgc_antismash_databases || !params.bgc_antismash_installationdirectory ) && !params.bgc_skip_antismash && ( session.config.conda && session.config.conda.enabled ) ) {
log.warn "[nf-core/funcscan] Running antiSMASH download database module, and detected conda has been enabled. Assuming using conda for pipeline run. Check config if this is not expected!"
}

}

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