0.2.6

Merge pull request #30 from 4dn-dcic/dev

Dev

0.2.5

.

0.2.4

• 4DN Annotations in repli-seq cwl.

0.2.3

• 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.

0.2.2

• Working CWL files for Repli-seq steps are included in cwl_awsem/repliseq.
• The output of the runs based on these CWL files are tested to be identical to the run based on https://github.com/dvera/shart/tree/8723ca835a3d739f75c33778040f6fcc3e5f992e up to log2ratio and the final outputs (normalize and smoothe) are statistically identical (randomization involved) according to visual inspection.

0.2.1

• WDL support/test

0.2.0

revised benchmark for partc

0.1.9

• added cooler mem calculation to partb benchmark

0.1.8

• Benchmark for hi-c-processing-partb added and tested.

0.1.7

• addfragtopairs cwl revised and tested
• Benchmark for addfragtopairs added and tested.