Important! Template update for nf-core/tools v3.0.2 #421
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jasmezz
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Oct 23, 2024
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| author: Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James | ||
| A. Fellows Yates |
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Should this be a single line? (The first one is 82 characters right now.)
| @@ -40,8 +40,8 @@ process { | |||
| enabled: params.save_db, | |||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | |||
| ] | |||
| ext.args = [ | |||
| params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files" , | |||
| ext.args = [ | |||
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Is that to align with ext.prefix and publishDir? Intense Harshil alignment! ™️ 😃
| "--min-len ${params.bgc_mincontiglength}" | ||
| ].join(' ').trim() | ||
| } | ||
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| withName: PROKKA { | ||
| ext.prefix = { "${meta.id}_prokka" } // to prevent pigz symlink problems of input files if already uncompressed during post-annotation gzipping |
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I wouldn't mind leaving comments like this as reminders, but no strong opinion.
| resourceLimits = [ | ||
| cpus: 4, | ||
| memory: '15.GB', | ||
| time: '1.h' |
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1h limit might be problematic for slow downloads (e.g. amrfinderplus database)? All test profiles got updated with the same values, are they mandatory?
| 'https://depot.galaxyproject.org/singularity/macrel:1.2.0--pyh5e36f6f_0': | ||
| 'biocontainers/macrel:1.2.0--pyh5e36f6f_0' }" | ||
| 'https://depot.galaxyproject.org/singularity/macrel:1.4.0--pyh7e72e81_0': | ||
| 'biocontainers/macrel:1.4.0--pyh7e72e81_0' }" |
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Update changelog with Macrel version update
| 'https://depot.galaxyproject.org/singularity/multiqc:1.24--pyhdfd78af_0' : | ||
| 'biocontainers/multiqc:1.24--pyhdfd78af_0' }" | ||
| 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : | ||
| 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" |
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Update changelog with multiqc version update
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| taxa_classification_mmseqs_taxonomy_sensitivity = 5.0 | ||
| taxa_classification_mmseqs_taxonomy_orffilters = 2.0 |
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Did you test this? Referring to the issue of floats getting reformatted to scientific or int notation that we had once.
| } | ||
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| // 3. Give warning if not using container system assuming conda | ||
| if ( params.run_bgc_screening && ( !params.bgc_antismash_db ) && !params.bgc_skip_antismash && ( session.config.conda && session.config.conda.enabled ) ) { |
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The CI errors all come from a (recent) faulty database update for one tool of the AMP workflow described in #423. Thus, only those CI tests without the AMP workflow succeed atm. All others will fail until either
For template update purposes I am not sure if the database issue is required to be solved first? |
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Version
3.0.2of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-3.0.2branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.
For more information about this release of nf-core/tools, please see the
v3.0.2release page.