system disk and tmp directory

[antoine4ucsd]

Hello great work with this tool. I made it work for several samples but having space/tmp dir problems with a larger samples I tried to adapt according to your tip my code as follow (singularity mode since docker not available on my server)

cwltool   --tmp-outdir-prefix=/mypath/_virtus/tmp_cwl2/ \
               --tmpdir-prefix=/mypath/_virtus/tmp_cwl2/  \
               --rm-tmpdir \
               --singularity  \
                ./VIRTUS.PE.cwl  VIRTUS.PE.localref.job2.yaml

and the yaml file is

fastq1:
  class: File
  path: >-
    /mypath/_virtus/VIRTUS2/wrapper/JFXLNRLG1_SPL_1.fastq.gz
fastq2:
  class: File
  path: >-
    /mypath/_virtus/VIRTUS2/wrapper/JFXLNRLG1_SPL_2.fastq.gz
genomeDir_human:
  class: Directory
  path: /mypath/_virtus/STAR_index_human_localref
genomeDir_virus:
  class: Directory
  path: /mypath/_virtus/STAR_index_virus_localref
nthreads: 40
outFileNamePrefix_human: human
filename_output: virtus2.filename.localref.output.tsv

but I still get these subfolder being created , each of them containing fastq (up to 300Go each ) and the former subdir are NOT removed. I thought the --rm-tmpdir would work?

THANK YOU!

[yyoshiaki]

Hi,

It sounds weird. --rm-tmpdir sounds reasonable. It may be due to singularity, but I don't have any idea, to be honest... Because this is issue relating to cwltool, it may be a solution to open an issue in cwltool repository.

[antoine4ucsd]

ok. thank you