Replace tmp_dir directory in BaseRecalibration

[FriederikeHanssen]

nf-core/sarek pull request

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I experienced issues with the option --tmp_dir in the process BaseRecalibration being hardcoded to /tmp since in our setup this directory is not big enough. We use the setting scratch=true or scratch = /my/directory/ instead, which writes the intermediate files there. In an initial discussion, we agreed on using ${TMPDIR:-/tmp}, however I still experienced issues: when testing with scratch = /my/directory/, intermediate files were still written to tmp.

For the process MarkDuplicates the setting is --TMP_DIR = . . I tested the same for BaseRecalibration. This results in:

scratch = true : Intermediate files are written to /scratch
scratch = /my/dir: Intermediate files are written to the directory
scratch = false: Intermediate files are written to a tmp directory within the work-dir

This behaviour appears desirable to me and is somewhat in line with Harshil's proposal to always specify the work directory.

[FriederikeHanssen]

@maxulysse tried this again by deleting and re-forking. Hope all is well now with the not overwriting your changes.

[maxulysse]

This one is perfect.
Thanks a lot