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Commit 0706a827 authored by Valentina Galata's avatar Valentina Galata
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assembly: updated input (preproc files); operams update; not finished - polishing/filtering

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workflow/rules/assembly.smk
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workflow/steps/assembly.smk
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......@@ -2,17 +2,13 @@
include:
"../rules/assembly.smk"
include:
"../rules/mapping.smk"
# include:
# "../rules/mapping.smk"
rule ASSEMBLY:
input:
# lr=expand(os.path.join(RESULTS_DIR, "assembly/lr/{tool}/ASSEMBLY.FILTERED.fasta"), tool=config["assemblers"]["lr"]),
# sr=expand(os.path.join(RESULTS_DIR, "assembly/sr/{tool}/ASSEMBLY.FILTERED.fasta"), tool=config["assemblers"]["sr"]),
# hy=expand(os.path.join(RESULTS_DIR, "assembly/hy/{tool}/ASSEMBLY.FILTERED.fasta"), tool=config["assemblers"]["hy"]),
# hyhy=expand(os.path.join(RESULTS_DIR, "assembly/hyhy/{tool}/ASSEMBLY.FILTERED.fasta"), tool=config["assemblers"]["hyhy"]),
expand(
os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.FILTERED.fasta"),
os.path.join(RESULTS_DIR, "assembly/{rtype_tool}/ASSEMBLY.fasta"),
rtype_tool=["%s/%s" % (rtype, tool) for rtype, tool in READ_ASSEMBLERS],
)
output:
......
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