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Commit 0977c6d2 authored by Jules Sabban's avatar Jules Sabban
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Change modules for genobioinfo usability

parent 5f90cbc2
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1 merge request!15genologin -> genobioinfo
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......@@ -21,10 +21,8 @@ I_NAMES=$2 # path to chrom_names file
R_PATTERN=$3 # chr pattern to remove from bedgraph file
#### MODULES ####
module load bioinfo/samtools-1.16.1
module load bioinfo/bedtools-2.27.1
module load bioinfo/samtools/1.18
module load bioinfo/bedtools/2.27.1
replace_chr_names() {
# replace chr names
......@@ -82,7 +80,7 @@ remove_unwanted_scaffold(){
main() {
BAM=$(find $I_DIR -type f -name '*R1*unmerged.bam' -execdir basename '{}' ';'|sed -n ${SLURM_ARRAY_TASK_ID}p)
BAM=$(find $I_DIR -type f -name '*unmerged.bam' -execdir basename '{}' ';'|sed -n ${SLURM_ARRAY_TASK_ID}p)
echo -e "Traitement de ${BAM}"
BAM_PATH="${I_DIR}/${BAM}"
......@@ -97,4 +95,4 @@ main() {
remove_unwanted_scaffold
}
main
\ No newline at end of file
main
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