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Garbage collect temporary files #79

unode opened this issue Sep 10, 2018 · 0 comments

Garbage collect temporary files #79

unode opened this issue Sep 10, 2018 · 0 comments


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@unode unode commented Sep 10, 2018

When running ngless, files are accumulated in the temporary directory until the entire computation is complete at which point they are deleted from disk.
With sufficiently large scripts (or large inputs) it's easy to run out of storage in this location.

Can we implement some kind of garbage collecting solution that removes files from --temporary-directory once no additional computation depends on them?

@luispedro luispedro closed this in 151ba9b Oct 28, 2018
luispedro added a commit that referenced this issue Nov 12, 2018
Many small fixes rather than any large new features.

Full ChangeLog:

    * Fix to lock1's return value when used with paths (#68 - reopen)
    * Support _F/_R suffixes for forward/reverse in load_mocat_sample
    * samtools_sort() now accepts by={name} to sort by read name
    * Fixed bug where header was printed even when STDOUT was used
    * Fixed bug where writing interleaved FastQ to STDOUT did not work as
    * Indices created by bwa and minimap2 are now versioned
    * arg1 in external modules is no longer always treated as a path
    * Added expand_searchpath to external modules API (closes #56)
    * Fixed bug where detection of Fastq encoding was not performed on the second pair
    * Fix saving fastq sets with --subsample (issue #85)
    * Add __extra_megahit_args to assemble() (issue #86)
    * Better error message when user mis-specifies the ngless version string
    (issue #84)
    * Support NO_COLOR environment variable (issue #83)
    * Garbage collection for temporary files (issue #79)
    * Rename --search-dir to --search-path for consistency with other API
    * Fix corner case with select() producing incorrect CIGAR strings (#92)
    * Always check output file writability (#91)
    * Make paired() accept encoding argument
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