Commit 051ab5e0 authored by mmassaviol's avatar mmassaviol
Browse files

Debug (zcat -f to also use uncompressed files)

parent e235b6ba
......@@ -207,10 +207,10 @@ rule jellyfish_count:
files = ""
if (config["SeOrPe"] == "PE"):
for r1,r2 in zip(inputs["read"],inputs["read2"]):
files += "<(zcat "+r1+") <(zcat "+r2+") "
files += "<(zcat -f "+r1+") <(zcat -f "+r2+") "
else:
for r in inputs["read"]:
files += "<(zcat "+r+") "
files += "<(zcat -f "+r+") "
shell(
"jellyfish count "+
"{params.canonical_kmer} "+
......
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