job_tractmaps

#!/bin/bash

subject=$1


module load gcc/9.3.0 fsl

#copy everything to tmpdir
mkdir -p $SLURM_TMPDIR/results/diffparc $SLURM_TMPDIR/results/hcp_mmp
cp -Rv config resources workflow $SLURM_TMPDIR
cp -Rv results/diffparc/${subject} $SLURM_TMPDIR/results/diffparc/
cp -Rv results/diffparc/tpl* $SLURM_TMPDIR/results/diffparc/
cp -Rv results/hcp_mmp/${subject} $SLURM_TMPDIR/results/hcp_mmp/
cp -Rv results/hcp_mmp/tpl* $SLURM_TMPDIR/results/hcp_mmp/

pushd $SLURM_TMPDIR
snakemake --touch -j1  #touch the files to make sure 

targets=''
for k in `seq 2 7`
do
    targets="$targets results/tractmap/${subject}/${subject}_space-MNI152NLin6Asym_label-fullBF_method-spectralcosine_k-${k}_tractmap4d.nii.gz"
done

snakemake --use-singularity --singularity-args='\-e' --singularity-prefix /project/6050199/akhanf/singularity/snakemake_containers/ --rerun-incomplete --keep-going --show-failed-logs --resources gpus=1 -j8 $targets
popd

#copy tractmap results from tmpdir to this dir
mkdir -p results/tractmap 
cp -Rv $SLURM_TMPDIR/results/tractmap/${subject} results/tractmap/