From b7c628aa1df65e577f9f33c5a001fc26f1322293 Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Tue, 6 Oct 2020 09:07:05 +0200 Subject: [PATCH] Wrong percentage escape attempt. --- smwrappers/explore_mapping_parameters/wrapper.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/smwrappers/explore_mapping_parameters/wrapper.py b/smwrappers/explore_mapping_parameters/wrapper.py index 7f94718..0cebcfc 100644 --- a/smwrappers/explore_mapping_parameters/wrapper.py +++ b/smwrappers/explore_mapping_parameters/wrapper.py @@ -27,7 +27,7 @@ def mapping_command(aligner): cmd="niceload --noswap -q hisat2 -p {snakemake.threads} --dta --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null" echo ${{cmd}} 1> {snakemake.log.log} eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err} -rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%%" -f1) +rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%" -f1) echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record} """ elif aligner == "bowtie2": @@ -36,7 +36,7 @@ echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rat cmd="niceload --noswap -q bowtie2 -p {snakemake.threads} --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null" echo ${{cmd}} > {snakemake.log.log} eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err} -rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%%" -f1) +rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%" -f1) echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record} """ # elif aligner == "crac": -- GitLab