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CODON migration changes. #40
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Small changes to adjust the pipeline infrastructure to CODON
tools/Assembly/antismash/chunking_antismash_with_conditionals/antismash/run_antismash_short.sh
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"owltools", | ||
"faselector", | ||
"format_bedfile", | ||
"trimmomatic", |
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I think we should add '.sh' extensions to add_header, awk_tool, format_bedfile and trimmomatic
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Yeah, I'll do that :).
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Thank you, Martin, for structuring all these scripts! That makes life easier
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Changes are appropriate, clean-up is fine, and adding error exceptions for BASH options is a must, however, the antismash script could be a CWL tool but it is not a priority.
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changes are ok, porting python v2 to v3 should be a separate task in pipeline 5.1
Small changes to adjust the pipeline infrastructure to CODON