Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat: Update start_HG_marvin.sh #39

Merged
merged 2 commits into from
Sep 4, 2023
Merged

feat: Update start_HG_marvin.sh #39

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
67571f6
feat: Update start_HG_marvin.sh
padraicc Aug 31, 2023
444bbb3
fix: add bam index a input for CNVpytor
padraicc Sep 4, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 9 additions & 4 deletions start_HG_marvin.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,18 +1,23 @@
#!/usr/bin/env bash
# To run script:
# bash /projects/wp3/nobackup/TWIST/Bin/Poirot/start_TE_marvin.sh /projects/wp3/nobackup/WGS/*/230619_NDX550925_RUO_0133_AHJ2YMBGXT/Sample_* HG4
# bash /projects/wp3/nobackup/TWIST/Bin/Poirot/start_HG_marvin.sh /projects/wp3/nobackup/WGS/*/230619_NDX550925_RUO_0133_AHJ2YMBGXT/Sample_* HG4

set -euo pipefail

module load slurm-drmaa/1.1.3
module load snakemake/7.22.0
module load singularity/3.7.1
source /beegfs-storage/projects/wp3/nobackup/TWIST/Bin/Poirot/hydra-env/bin/activate;
pip install -r /beegfs-storage/projects/wp3/nobackup/TWIST/Bin/Poirot/requirements.txt

poirotFolder=/beegfs-storage/projects/wp3/nobackup/TWIST/Bin/Poirot

python3.9 -m venv ${poirotFolder}/hydra_env
source ${poirotFolder}/hydra_env/bin/activate
pip install -r ${poirotFolder}/requirements.txt

fastqFolder=$1
sequencerun=$2 #Sequence ID
startDir=$PWD

poirotFolder=/beegfs-storage/projects/wp3/nobackup/TWIST/Bin/Poirot
outbox=$(echo $(echo ${poirotFolder} | rev | cut -d/ -f3- | rev)/OUTBOX)

# Create outbox and scratch folders
Expand Down
Loading