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mmassaviol
WAWmassaviol
Commits
b66322cb
Commit
b66322cb
authored
Oct 04, 2021
by
khalid
Browse files
Change htseq-count name
parent
140f52b8
Changes
3
Hide whitespace changes
Inline
Side-by-side
tools/hisat2_index/hisat2_index.yaml
View file @
b66322cb
...
...
@@ -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
:
{
...
...
tools/htseq
-
count/htseq
-
count.rule.snakefile
→
tools/htseq
_
count/htseq
_
count.rule.snakefile
View file @
b66322cb
...
...
@@ -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:
...
...
tools/htseq
-
count/htseq
-
count.yaml
→
tools/htseq
_
count/htseq
_
count.yaml
View file @
b66322cb
...
...
@@ -27,7 +27,7 @@
options
:
[
{
name
:
htseq
-
count_minaqual
,
name
:
htseq
_
count_minaqual
,
prefix
:
-a
,
type
:
numeric
,
value
:
10
,
...
...
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