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Pass arguments through to megahit #86

luispedro opened this issue Oct 14, 2018 · 0 comments

Pass arguments through to megahit #86

luispedro opened this issue Oct 14, 2018 · 0 comments


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There should be a semi-hidden way to pass arguments to megahit like __bwa_extra_args does for map().

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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