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wtsi-npg / p4

Process and Pipe Pipeline Panacea
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markdup_method:none for phix and non-consented human split #304

Closed dozy closed 2 years ago

dozy commented 2 years ago

for phix (by alignment) and non-consented human split: force markdup_method to "none", with primer_clip_method set to "no_clip"; and reference_genome_fasta (used by calmd) set to the value of parameter "phix_reference_genome_fasta" for phix and to the value of parameter "hs_reference_genome_fasta" for non-consented human

remove --reference flag from calmd command in markdup_none - this is both unnecessary and causes problems when combining markdup_method:none with no_target_alignment