Skip to content
Projects
Groups
Snippets
Help
This project
Loading...
Sign in / Register
Toggle navigation
S
STR
Project
Project
Details
Activity
Cycle Analytics
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Charts
Issues
0
Issues
0
List
Board
Labels
Milestones
Merge Requests
0
Merge Requests
0
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Charts
Wiki
Wiki
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Charts
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
Anne-Sophie Denommé-Pichon
STR
Commits
dc46dad7
Commit
dc46dad7
authored
Feb 15, 2020
by
Anne-Sophie Denommé-Pichon
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Add script to generate manifest by patient for EHDN
parent
c9d1fe18
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
36 additions
and
0 deletions
+36
-0
ehdn_getmanifest.sh
ehdn/ehdn_getmanifest.sh
+36
-0
No files found.
ehdn/ehdn_getmanifest.sh
0 → 100755
View file @
dc46dad7
#! /bin/sh
### ASDP PIPELINE ###
## ehdn_getmanifest.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to generate automatically a manifest by patient in a tsv format
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20200215
## last revision date : 20200215
## Known bugs : None
WORKDIR
=
"/work/gad/shared/analyse/STR/pipeline"
cd
"
$WORKDIR
"
# Generate manifest by patient for all patients (to write file)
for case
in
dijen
*
do
# Generate manifest for one patient with all samples (to write lines in the file)
for
dijen
in
dijen
*
do
if
[
"x
$dijen
"
=
"x
$case
"
]
then
echo
-e
"
$dijen
\t
case
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
else
echo
-e
"
$dijen
\t
control
\t
$WORKDIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
fi
done
>
"
$WORKDIR
/
$case
/ehdn/
$case
.manifest.tsv"
done
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment