feat: create task/sample specific folder within each job that uses scratch dir

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

MIT License

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Not all users may have a job-specific variable like $SCRATCH or $TMPDIR that can be set in the config.yaml file (e.g. #26). To account for this, create working/scratch folders within the scratch/ directory to avoid errors.

~/path/to/scratch/
  |--assemblies/
     |--sample1/
     |--sample2/
     ...

Needs to be implemented in rules that expand wildcards and use scratch/:

megahit
crossMap
kallistoIndex
crossMap3
concoct
metabat
metabatCross
maxbin
maxbinCross
binRefine
binReassemble
abundance
GTDBtk
carveme
smetana
memote
grid
prokka
roary

franciscozorrilla / metaGEM

feat: create task/sample specific folder within each job that uses scratch dir #30