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@vivekbhr vivekbhr released this 08 Sep 09:37
· 4009 commits to master since this release
  • added --fastqc and --bw-binsize parameters to DNA-mapping wrapper script
  • additional organisms are now supported by adding new genome.py files
  • defined (effective) genome size as (genome length)-(number of 'N's) in genome.py files
  • simplified cluster submission by taking 'threads' parameter from rule definition, removed cluster.yaml
  • added DNA-mapping example configuration yaml file
  • added function get_fragment_length() to DNA-mapping internals.snakefile to parse median insert size from Picard output
  • added deepTools_qc.snakefile as one common snakefile for all deepTools rules,
    moved all deepTools rules from ChIP-seq Snakefile and computeGCBias.snakefile
  • moved include statements of module snakefiles from rules.snakefile to DNA-mapping Snakefile to simplify structure, removed rules.snakefile
  • renamed functions do_TrimGalore(trim) and do_InsertSizeMetrics(paired) in DNA-mapping Snakefile
  • renamed load_organisms.snakefile to load_organism_data.py
  • removed debugging.snakefile as it was not used by any pipeline
  • removed --local-cores parameter from all wrapper scripts as there are no local snakemake rules defined
  • many small other changes