Commit 95572a20 authored by Thomas  BIGOT's avatar Thomas BIGOT

metaphlan improvements

parent a63e8d01
......@@ -34,7 +34,7 @@ rule all:
expand(f"{reportsDir}/centrifuge_reportk-{{dbname}}.tsv",dbname=config["microbiome"]["centrifuge"]["db"]),
expand(f"{reportsDir}/centrifuge_krona-{{dbname}}.html",dbname=config["microbiome"]["centrifuge"]["db"]),
expand(f"{dataDir}/centrifuge_classification-report-{{dbname}}.tsv.bz2",dbname=config["microbiome"]["centrifuge"]["db"]),
f"{reportsDir}/{name}_metaphlan2_report.tsv",
f"{reportsDir}/metaphlan2_report.tsv",
expand(f"{reportsDir}/kraken2_report-{{dbname}}.tsv",dbname=config["microbiome"]["kraken2"]["db"]),
expand(f"{reportsDir}/kraken2_krona-{{dbname}}.html",dbname=config["microbiome"]["kraken2"]["db"]),
expand(f"{dataDir}/kraken2_classified-{{dbname}}.fq.bz2",dbname=config["microbiome"]["kraken2"]["db"]),
......@@ -179,7 +179,7 @@ rule metaphlan2:
benchmark:
"logs/benchmark/metaphlan2.tsv"
threads:
10
28
input:
"merged_trimmed_reads/R1R2.fastq"
output:
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment