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Pathogen-Genomics-Cymru / lodestone

Mycobacterial pipeline
GNU Affero General Public License v3.0
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Empty contaminants.fa in preprocessing:downloadContamGenomes #20

Closed annacprice closed 1 year ago

annacprice commented 1 year ago

Observed that sometimes contaminants.fa is empty (due to failed download) and no error is thrown in preprocessing:downloadContamGenomes

annacprice commented 1 year ago

N.B. Strict error checking is currently disabled for preprocessing:downloadContamGenomes in the nextflow.config.

https://github.com/Pathogen-Genomics-Cymru/tb-pipeline/blob/925f8b7667dc36afad90bf9b6b21d5e35adac32a/nextflow.config#L76

These lines can be removed from the config as they're no longer needed

WhalleyT commented 1 year ago

retry strategy added in PR #30