---
global:
- ROOT: /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA
- indir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/DATA
- outdir: /home/jillian/projects/perl/BioX-Workflow/example/bydir/OUT
- file_rule: (SAMPLE.*)$
- by_sample_outdir: 1
- find_by_dir: 1
rules:
- copy1:
local:
- INPUT: "{$self->indir}/{$sample}.csv"
- TRIMMOMATIC: "{$self->ROOT}/{$sample}_TRIMMOMATIC_THING.gz"
- before_meta: "\n#HPC mem=24GB"
process: |
echo "Working on {$self->{indir}}/{$sample}.csv"
cp "{$self->INPUT}" "{$self->{outdir}}/{$sample}.csv"
- copy2:
local:
- indir: "{$self->ROOT}"
- INPUT: "{$self->indir}/{$sample}.csv"
- before_meta: |
HPC THINGS
#
#HPC mem=24GB
#
process: |
echo "Working on {$self->{indir}}/{$sample}.csv" && \
echo "This should be UNDEF {$self->TRIMMOMATIC}" && \
cp "{$self->{indir}}/{$sample}.csv" "{$self->{outdir}}/{$sample}.csv"