Commit 7409a495 authored by Valentina Galata's avatar Valentina Galata
Browse files

issue #27: fixed targets for the MG-only case - PE vs. SE [ci skip]

parent df14b649
Pipeline #45810 skipped
......@@ -22,8 +22,8 @@ if config['eukdetect']['run_eukdetect']:
# master command
if MG or MT: # TODO: why not only MG as in ../mt/Taxonomy.smk?
tax_ctrl = expand(
"Analysis/taxonomy/kraken/{type}.kraken.{outfile}",
type=TYPES, outfile=["output.gz", "report"]
"Analysis/taxonomy/kraken/{type}.{kname}.{outfile}",
type=TYPES, kname=['kraken', 'se.kraken'] if len(MG) > 1 else ['kraken'], outfile=["output.gz", "report"]
)
tax_ctrl.append(expand("Analysis/taxonomy/mOTUs/{type}.mOTU.counts.tsv",type=TYPES))
if config['eukdetect']['run_eukdetect']:
......@@ -36,8 +36,8 @@ if CONTIGS:
tax_ctrl = ["Analysis/taxonomy/kraken/%s.kraken.parsed.tsv" % ASS]
if MG or MT:
tax_ctrl.append(expand(
"Analysis/taxonomy/kraken/{type}.kraken.{outfile}",
type=TYPES, outfile=["output.gz", "report"]
"Analysis/taxonomy/kraken/{type}.{kname}.{outfile}",
type=TYPES, kname=['kraken', 'se.kraken'] if len(MG) > 1 else ['kraken'], outfile=["output.gz", "report"]
))
if "analysis" in IMP_STEPS:
tax_ctrl.append("Analysis/taxonomy/mOTU_links/intermediary.tar.gz")
......
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