#!/bin/bash --login
#This example use general SBATCH settings, but please refer to the specific guide
#of intended the cluster for possible needed changes
#
# SLURM directives
#
# This is an array job with 35 subtasks, (--array=0-34).
#
# The output for each subtask will be sent to a separate file
# identified by the jobid (--output=array-%j.out)
#
# Each subtask will occupy one node (--nodes=1) with
# a wall-clock time limit of twenty minutes (--time=00:20:00)
#
# Replace [your-project] with the appropriate project name
# following --account (e.g., --account=project123)
#SBATCH --account=[your-project]
#SBATCH --output=array-%j.out
#SBATCH --array=0-34 #this should match the number of input files
#SBATCH --nodes=1
#SBATCH --ntasks=1 #One main task per file to be processed in each array-subtask
#SBATCH --cpus-per-task=1 #this will vary depending on the requirements of the task
#SBATCH --mem=1840M #Needed memory per array-subtask (or use --exclusive for exclusive access)
#SBATCH --time=00:20:00
#---
echo "All jobs in this array have:"
echo "- SLURM_ARRAY_JOB_ID=${SLURM_ARRAY_JOB_ID}"
echo "- SLURM_ARRAY_TASK_COUNT=${SLURM_ARRAY_TASK_COUNT}"
echo "- SLURM_ARRAY_TASK_MIN=${SLURM_ARRAY_TASK_MIN}"
echo "- SLURM_ARRAY_TASK_MAX=${SLURM_ARRAY_TASK_MAX}"
echo "This job in the array has:"
echo "- SLURM_JOB_ID=${SLURM_JOB_ID}"
echo "- SLURM_ARRAY_TASK_ID=${SLURM_ARRAY_TASK_ID}"
#---
#Specific settings for the cluster you are on
#(Check the specific guide of the cluster for additional settings)
#---
# grab our filename from a directory listing
FILES=($(ls -1 *.input.txt)) #this pulls in all the files ending with input.txt
FILENAME=${FILES[$SLURM_ARRAY_TASK_ID]} #this allows the slurm to enter the input.txt files into the job array
echo "My input file is ${FILENAME}" #this will print the file name into the log file
#---
#example job using the above variables
srun -N 1 -n 1 -c 1 ExpansionHunterDenovo-v0.8.7-linux_x86_64/scripts/casecontrol.py locus \
--manifest ${FILENAME} \
--output ${FILENAME}.CC_locus.tsv |