<commit_before>#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=XX_THREAD_COUNT_XX
#SBATCH --ntasks=1
#SBATCH --mem=XX_MEM_XX
#SBATCH --workdir="/mnt/SCRATCH/"

function cleanup (){
    echo "cleanup tmp data";
    sudo rm -rf $basedir;
}

input_id="XX_INPUTID_XX"
project="XX_PROJECT_XX"
md5="XX_MD5_XX"
s3_url="XX_S3URL_XX"
s3_profile="XX_S3PROFILE_XX"
s3_endpoint="XX_S3ENDPOINT_XX"

thread_count="XX_THREAD_COUNT_XX"
java_heap="XX_JAVAHEAP_XX"

basedir=`sudo mktemp -d genomel.hc.XXXXXXXXXX -p /mnt/SCRATCH/`
refdir="XX_REFDIR_XX"
s3dir="XX_S3DIR_XX"

repository="<EMAIL>:uc-cdis/cwl.git"
sudo chown ubuntu:ubuntu $basedir

cd $basedir

sudo git clone -b feat/slurm $repository genomel_cwl
sudo chown ubuntu:ubuntu -R genomel_cwl

trap cleanup EXIT

/home/ubuntu/.virtualenvs/p2/bin/python genomel_cwl/slurm/genomel_hc_pipeline.py \
--input_id $input_id \
--project $project \
--md5 $md5 \
--s3_url $s3_url \
--s3_profile $s3_profile \
--s3_endpoint $s3_endpoint \
--basedir $basedir \
--refdir $refdir \
--cwl $basedir/genomel_cwl/workflows/recalibration-workflow.cwl.yaml \
--s3dir $s3dir \
--thread_count $thread_count \
--java_heap $java_heap<commit_msg>fix(slurm): fix cwl tool path<commit_after>#!/bin/bash
#SBATCH --nodes=1
#SBATCH --cpus-per-task=XX_THREAD_COUNT_XX
#SBATCH --ntasks=1
#SBATCH --mem=XX_MEM_XX
#SBATCH --workdir="/mnt/SCRATCH/"

function cleanup (){
    echo "cleanup tmp data";
    sudo rm -rf $basedir;
}

input_id="XX_INPUTID_XX"
project="XX_PROJECT_XX"
md5="XX_MD5_XX"
s3_url="XX_S3URL_XX"
s3_profile="XX_S3PROFILE_XX"
s3_endpoint="XX_S3ENDPOINT_XX"

thread_count="XX_THREAD_COUNT_XX"
java_heap="XX_JAVAHEAP_XX"

basedir=`sudo mktemp -d genomel.hc.XXXXXXXXXX -p /mnt/SCRATCH/`
refdir="XX_REFDIR_XX"
s3dir="XX_S3DIR_XX"

repository="<EMAIL>:uc-cdis/cwl.git"
sudo chown ubuntu:ubuntu $basedir

cd $basedir

sudo git clone -b feat/slurm $repository genomel_cwl
sudo chown ubuntu:ubuntu -R genomel_cwl

trap cleanup EXIT

/home/ubuntu/.virtualenvs/p2/bin/python genomel_cwl/slurm/genomel_hc_pipeline.py \
--input_id $input_id \
--project $project \
--md5 $md5 \
--s3_url $s3_url \
--s3_profile $s3_profile \
--s3_endpoint $s3_endpoint \
--basedir $basedir \
--refdir $refdir \
--cwl $basedir/genomel_cwl/tools/variant_detection/haplotypecaller/HaplotypeCaller.cwl.yaml \
--s3dir $s3dir \
--thread_count $thread_count \
--java_heap $java_heap
{'fraction_non_alphanumeric': 0.14075010535187527, 'fraction_numerical': 0.01938474504846186, 'mean_word_length': 4.9054726368159205, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 2, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5415447', 'n_tokens_mistral': 1074, 'n_tokens_neox': 1038, 'n_words': 173}