diff --git a/workflow/Snakefile b/workflow/Snakefile index f9224fd..a820a07 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -147,6 +147,12 @@ elif assay in ["atac", "chip"]: rule_all_ins.extend(expand(join(ppqt_dir, "{name}.{ext}.ppqt"), name=samples, ext=tag_ext)) rule_all_ins.extend(expand(join(ppqt_dir, "{name}.{ext}.pdf"), name=samples, ext=tag_ext)) rule_all_ins.extend(expand(join(ppqt_dir, "{name}.{ext}.ppqt.txt"), name=samples, ext=tag_ext)) + rule_all_ins.extend(expand( + join(uropa_dir, "{application}", "{name}_uropa_{_type}_allhits.txt"), + name=chips, + application=["macsBroad"], + _type=peak_types, + )) elif assay == "atac": rule_all_ins.extend(expand( join(genrich_dir, "{name}", "{name}.narrowPeak"), name=chips @@ -180,7 +186,7 @@ if has_inputs: rule_all_ins.extend(expand( join(uropa_dir, "{application}", "{name}_uropa_{_type}_allhits.txt"), name=chips, - application=["macsNarrow", "macsBroad"], + application=["macsNarrow"], _type=peak_types, ))