---
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
process:
|
echo
"Working on {$self->{indir}}/{$sample}.csv"
&& \
echo
"This should be UNDEF {$self->TRIMMOMATIC}"
&& \
cp
"{$self->{indir}}/{$sample}.csv"
"{$self->{outdir}}/{$sample}.csv"