Processes abstracted into a shared file #28
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workflows/cath-shared.nf
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| params.cath_af_cli = 'cath-af-cli' | ||
| params.cath_version = 'v4_3_0' | ||
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| params.publish_dir = "$workflow.launchDir/cath-test-hpc-${params.dataset_name}" |
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This is probably workflow specific - maybe move this one back to the workflow?
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Actually, we could just make it less workflow specific:
params.publish_dir = "$workflow.launchDir/results-${params.dataset_name}"
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|Made that change and added results-*/ to gitignore
workflows/cath-shared.nf
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| path uniprot_id_file | ||
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| output: | ||
| path params.af_manifest_fn |
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I shouldn't have used a global variable here - creates an unnecessary dependency.
This could be any filename - and it's probably better that the process takes care of this internally:
output:
path 'manifest.txt'
"""
... > manifest.txt
"""
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Done and checked in
workflows/cath-shared.nf
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| path uniprot_domain_id | ||
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| output: | ||
| path params.uniprot_ids_csv_fn |
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Again, we aren't publishing the output file, so we don't need to use the global filename - probably better to replace this with 'uniprot_ids.txt' (and change the script to reflect)
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(sorry, I know this was my code!)
Closes #25