Newer
Older
# time to start doing work!
# step 0. load dependencies
# (curl, jq, and singularity/apptainer are preloaded on Puhti)
module load parallel
# step 1: transfer data in parallel
parallel --col-sep ' ' \
-a {work_dir}/{name}/transfer.txt \
java -Xmx256m \
-jar {globus_path} \
--spring.config.location={globus_parent_path}/config/ \
-s \{1} -d $TMPDIR --file_size \{2}
# the job _must be_ scheduled on a node with local storage
# it's cleaned up by the system after the job finishes
# can't use --chdir, $TMPDIR is set when the job starts
# step 2: run pgsc_calc and calculate some scores
nextflow run {pgsc_calc_dir} -profile singularity \
--min_overlap 0.01 \
--max_cpus 40 \
--max_memory "32.GB" \
--parallel
# step 3: report job status to INTERVENE platform
# (automatically executed in callback_exit_handler by trap)
# ------------------------------------------------------------------------------