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Support compressing output files with collect() #42

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unode opened this issue Nov 9, 2017 · 0 comments

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@unode
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commented Nov 9, 2017

Using:

collect(counted,
        current=sample,
        allneeded=readlines(all_samples),
        ofile=outputdir + '/' + sample + '.tsv.gz')

Produced a sample.tsv.gz file that was not gzipped.
However collect() uses .gz internally for its partial files.

@luispedro luispedro closed this in 26d86c2 Feb 1, 2019

luispedro added a commit that referenced this issue Feb 22, 2019

RLS Release 0.11.0
A collection of several bugfixes and performance improvements over the
last few months.

Full ChangeLog:

    * Switch to diagrams package for plotting
    * Update minimap2 version to 2.14
    * Module samtools (version 0.1) now includes samtools_view
    * Update to LTS-13 (GHC 8.6)
    * Fix bug with orf_find & prots_out argument
    * Call bwa/minimap2 with interleaved fastq files
    * Add --verbose flag to check-install mode
    * Avoid leaving open file descriptors after FastQ encoding detection
    * Fix bug in garbage collection
    * Compress intermediate SAM files (#22)
    * Tar extraction uses much less memory (#77)
    * Add early checks for input files in more situations (#33)
    * Support compression in collect() output (#42)
    * Fix CIGAR (#92) for select() blocks

luispedro added a commit that referenced this issue Mar 15, 2019

RLS Release 0.11.0
A collection of several bugfixes and performance improvements over the
last few months.

Full ChangeLog:

    * Switch to diagrams package for plotting
    * Update minimap2 version to 2.14
    * Module samtools (version 0.1) now includes samtools_view
    * Fix bug with orf_find & prots_out argument
    * Call bwa/minimap2 with interleaved fastq files
    * Add --verbose flag to check-install mode
    * Avoid leaving open file descriptors after FastQ encoding detection
    * Fix bug in garbage collection
    * Compress intermediate SAM files (#22)
    * Tar extraction uses much less memory (#77)
    * Add early checks for input files in more situations (#33)
    * Support compression in collect() output (#42)
    * Fix CIGAR (#92) for select() blocks
    * Update to LTS-13 (GHC 8.6)
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