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Just copy to deal with shared filesystems
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currocam committed Apr 23, 2024
1 parent b463b0b commit f58be07
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion workflow/scripts/emu_combine.py
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,9 @@
if not temp_basename.endswith("_rel-abundance.tsv"):
temp_basename = os.path.splitext(temp_basename)[0] + "_rel-abundance.tsv"
temp = os.path.join(tmpdir, temp_basename)
os.link(infile, temp)
shell("cp {infile} {temp}")
# Sadly, shared filesystem didn't like previous code
# os.link(infile, temp)
shell("emu combine-outputs {tmpdir} {rank} {extra} {log}")
if split and counts:
shell("mv {tmpdir}/emu-combined-taxonomy-{rank}.tsv {taxonomy}")
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