Added offline run flag and profile #29
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JoseEspinosa
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May 21, 2024
conf/offline.config
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| // Other parameters | ||
| offline_run = true | ||
| local_databases = true |
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Don't you need also to provide here the paths to the local DBs?
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I don't think I can. I have no prior knowledge of the file structure on the user's machine.
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As discussed on slack I was referring of creating a small version of the databases for running a test using the offline mode
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Done now, see test_offline.config
| ch_samplesheet_fasta.ifEmpty { | ||
| fasta_input = true | ||
| } | ||
| if (fasta_input && params.offline_run) { |
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Do we want to through a warning here instead making clear that using fasta could have an impact on the rate limit if too many files are provided?
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
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Closes #28
offline_runoptionofflineprofileNote: the options only affect the ortholog fetching, downstream still requires network. FASTA input is not available for offline runs for now.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).