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chipseq_analysis
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BICF
Astrocyte
chipseq_analysis
Commits
8fba6bd9
Commit
8fba6bd9
authored
4 years ago
by
Venkat Malladi
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Add usage statement.
parent
d9e3b2b4
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1 merge request
!67
Resolve "Rename Plot profile to be consistent with naming"
Pipeline
#6322
failed with stages
in 7 hours, 36 minutes, and 1 second
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2 changed files
workflow/main.nf
+1
-2
1 addition, 2 deletions
workflow/main.nf
workflow/scripts/plot_profile.sh
+29
-1
29 additions, 1 deletion
workflow/scripts/plot_profile.sh
with
30 additions
and
3 deletions
workflow/main.nf
+
1
−
2
View file @
8fba6bd9
...
...
@@ -488,7 +488,6 @@ process plotProfile {
output:
file '*.{png,gz}' into plotProfile
file gtf from gtfFile
when:
...
...
@@ -497,7 +496,7 @@ process plotProfile {
script:
"""
module load deeptools/2.5.0.1
bash $baseDir/scripts/plot_profile.sh
bash $baseDir/scripts/plot_profile.sh
-g $gtfFile
"""
}
...
...
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workflow/scripts/plot_profile.sh
+
29
−
1
View file @
8fba6bd9
#!/bin/bash
#plot_profile.sh
script_name
=
"plot_profile.sh"
#Help function
usage
()
{
echo
"-h --Help documentation for
$script_name
"
echo
"-g --File path to gtf/bed files"
echo
"Example:
$script_name
-g 'genome.gtf'"
exit
1
}
raise
()
{
echo
"
${
1
}
"
>
&2
...
...
@@ -55,8 +66,25 @@ plot_profile() {
run_main
()
{
# Parsing options
OPTIND
=
1
# Reset OPTIND
while
getopts
:g:h opt
do
case
$opt
in
g
)
gtf
=
$OPTARG
;;
h
)
usage
;;
esac
done
shift
$((
$OPTIND
-
1
))
# Check for mandatory options
if
[[
-z
$gtf
]]
;
then
usage
fi
bws
=
$(
ls
*
.bw
)
gtf
=
$(
ls
*
.gtf
*
.bed
)
check_tools
||
exit
1
...
...
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