Commit bda364f2 authored by Valentina Galata's avatar Valentina Galata
Browse files

analysis: mmseqs2: bug fix (wrong db type) (issue #119); metap - whether faa output is tmp

parent 6e6e390a
......@@ -34,8 +34,8 @@ data:
r1: "/mnt/isilon/projects/ecosystem_biology/ONT_pilot/GDB_2019/metat/sr/FastSelectFull1_MT_Rashi_S14_R1_001.fastq.gz" # leave empty if no data, i.e. ""
r2: "/mnt/isilon/projects/ecosystem_biology/ONT_pilot/GDB_2019/metat/sr/FastSelectFull1_MT_Rashi_S14_R2_001.fastq.gz" # leave empty if no data, i.e. ""
# Meta-proteomics
# metap:
# TODO
metap:
"" # TODO
############################################################
# TOOLS
......
......@@ -339,7 +339,7 @@ rule analysis_mmseqs2:
)
output:
tsv=os.path.join(RESULTS_DIR, "analysis/mmseqs2/clusters.tsv"),
faa=temp(os.path.join(RESULTS_DIR, "analysis/mmseqs2/proteins.faa")),
faa=temp(os.path.join(RESULTS_DIR, "analysis/mmseqs2/proteins.faa")) if "metap" not in config["data"] else os.path.join(RESULTS_DIR, "analysis/mmseqs2/proteins.faa"),
tmpdir=temp(directory(os.path.join(RESULTS_DIR, "analysis/mmseqs2/tmp")))
log:
"logs/analysis.mmseqs2.log"
......@@ -358,7 +358,7 @@ rule analysis_mmseqs2:
# put all proteins together
"for f in {input}; do sed 's/^>/>'$(basename $(dirname ${{f}}))'__/' ${{f}}; done > {output.faa} && "
# DB, cluster, TSV output
"mmseqs createdb --dbtype 2 -v 3 {output.faa} {params.db} && "
"mmseqs createdb --dbtype 1 -v 3 {output.faa} {params.db} && "
"mmseqs linclust --threads {threads} {params.db} {params.cl} {output.tmpdir} && "
"mmseqs createtsv {params.db} {params.db} {params.cl} {output.tsv} && "
"date) &> {log}"
......
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