Verified Commit 17e92926 authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

preseq new version, use shell command

parent df14705a
......@@ -7,8 +7,10 @@ rule preseq_lc_extrap:
"-v {} -seed 1".format( "" if config["single_end"] else "-pe" )
log:
"logs/preseq/{sample}.log"
wrapper:
"0.64.0/bio/preseq/lc_extrap"
shell:
"""
preseq lc_extrap {params} -output {output} {input} 2> {log}
"""
rule collect_multiple_metrics:
input:
......@@ -199,7 +201,7 @@ rule phantompeakqualtools:
conda:
"../envs/phantompeakqualtools.yaml"
shell:
"( Rscript -e \"library(caTools); source('../workflow/scripts/run_spp.R')\" "
"( Rscript -e \"library(caTools); source('workflow/scripts/run_spp.R')\" "
" -c={input} -savp={output.plot} -savd={output.r_data} "
" -out={output.res_phantom} -p={threads} 2>&1 ) >{log}"
......
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