Commit b66322cb authored by khalid's avatar khalid
Browse files

Change htseq-count name

parent 140f52b8
......@@ -45,9 +45,9 @@
"wget -O hisat2-2.2.1-linux-x86_64.zip https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download",
"unzip hisat2-2.2.1-linux-x86_64.zip",
"mv hisat2-2.2.1 /opt/biotools/",
"rm -rf hisat2-2.2.1*"
"ENV PATH /opt/biotools/hisat2-2.2.1:$PATH "
"echo "export PATH=$PATH:/opt/biotools/hisat2-2.2.1" >> /etc/environment"
"rm -rf hisat2-2.2.1*",
"ENV PATH /opt/biotools/hisat2-2.2.1:$PATH ",
"echo \"export PATH=$PATH:/opt/biotools/hisat2-2.2.1\" >> /etc/environment"
],
},
citations: {
......
......@@ -7,7 +7,7 @@ rule <step_name>__htseq-count:
config["results_dir"]+'/logs/' + config["<step_name>__htseq-count_output_dir"] + '/{sample}_htseq-count_log.txt'
params:
command = config["<step_name>__htseq-count_command"],
htseq-count_minaqual = config["htseq-count_minaqual"],
htseq_count_minaqual = config["htseq-count_minaqual"],
htseq_stranded = config["htseq_stranded"],
output_dir = config["results_dir"]+'/'+config["<step_name>__htseq-count_output_dir"]
shell:
......
......@@ -27,7 +27,7 @@
options:
[
{
name: htseq-count_minaqual,
name: htseq_count_minaqual,
prefix: -a,
type: numeric,
value: 10,
......
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