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@SooLee SooLee released this 06 Dec 22:39
· 216 commits to master since this release
0.2.3
b6838d8
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Learn about vigilant mode.
  • All changes are related to the Repli-seq pipeline (cwl_awsem/repliseq)
    • A working pipeline repliseq-parta.cwl going from clip to count is ready now. It generates four output files - bam, filtered sorted bam, deduped bam and count bg.
    • Benchmark is available for repliseq-parta.
    • Minor changes
      • docker version v10
      • align se and pe are now merged - it turns out that a single fastq file is used even for paired-end data.
      • unused parameter MINSIZE is removed from count - I had replaced the part that uses this parameter with the use of a chromsize file.
      • NEXTRATHREADS in filtersort is now replaced with NTHREADS (NEXTRATHREADS = NTHREADS - 1) so that a global nthreads parameter can be used for both align and filtersort.
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