samtools_sort.submit

# Give Docker and argument and then set output, error, and log.
universe = Docker
docker_image = staphb/samtools
arguments = "$(RUN)"
executable = samtools_sort.sh

#output = samtools_sort_$(RUN).out
#error = samtools_sort_$(RUN).err
#log = samtools_sort_$(RUN).log

# Rules to transfer and transferring files
transfer_executable = TRUE
should_transfer_files = YES
when_to_transfer_output = ON_EXIT

staging_prefix = file:///staging/groups/pepperell_group/Mtb_RNAseq/HTSeqCounts
results_staging_prefix = file:///staging/groups/pepperell_group/Mtb_RNAseq/HTSeqCounts/Results

transfer_input_files = $(results_staging_prefix)/$(RUN).bam.gz
transfer_output_files = $(RUN).sort.bam.gz
transfer_output_remaps = "$(RUN).sort.bam.gz = $(results_staging_prefix)/$(RUN).sort.bam.gz"

# Resource request and Queue job
requirements = (Target.HasCHTCStaging==TRUE)
request_cpus = 1
request_memory = 4GB
request_disk = 50GB

queue