This repo contains a
slurm-pipeline specification
file (specification.json) and associated scripts for processing Lasse's
re-sequencing using BLAST (specifically, blastn).
It's assumed you've already run
the first pipeline on the
samples you're interested in. This pipeline expects to find its initial
input files in the 02-map/$task-unmapped.fastq.gz files from
that pipeline.
The 01-split/split.sh script expects the original unmapped sample FASTQ
files to be in ../../../initial/02-map/$task-unmapped.fastq.gz.
The scripts in 01-split, 02-blastn, etc. are all submitted by sbatch
for execution under SLURM. The final step,
03-panel leaves its output in 03-panel/out and
03-panel/summary-virus.
$ make clean-1Note that this throws away all the intermediate work done by the pipeline.
$ make clean-2Does a make clean-1 and removes intermediate SLURM output log files.
$ make clean-3Does a make clean-2 and also removes the final output in 03-panel/out.