Add script to generate manifest by patient for EHDN

parent c9d1fe18
#! /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\tcase\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
else
echo -e "$dijen\tcontrol\t$WORKDIR/$dijen/ehdn/$dijen.str_profile.json"
fi
done > "$WORKDIR/$case/ehdn/$case.manifest.tsv"
done
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