0.6.3

Bug fixes for python3.

v0.6.2: Merge pull request #63 from maxplanck-ie/develop

Bugfix for snakemake module.. Load a specific snakemake version to avoid local python error

0.6.1

• The allele-specific option is no longer on by default.

Tiger rattlesnake

• MAJOR CHANGES:

  • Allele-Specific mapping : Allele-specific DNA and RNA-mapping is now possible and both ChIP-Seq and RNA-seq pipeline can handle "allele_mapping" mode.
  • Differential binding : Differential binding can be performed using CSAW, both normal and allele-specific.
  • MultiQC : MultiQC summarizes QC results for DNA-mapping and RNA-mapping workflows.
  • R package : New R package called snakediff contains all functions for differential binding and expression. The DE functions have been
    transformed into clean and consistent layout, with docs.
  • Deeptools commands : All deeptools commands now moved into common deeptools_cmds module, and are shared between functions.

• MINOR CHANGES:

  • Wrappers have been formatted for easier readability.
  • chr X, Y, M and unmapped scaffolds are now ignored for normalization in bamCoverage (DNA-mapping) and bamCompare (Chip-Seq).
  • bamCompare outputs are named with suffix , instead of a static suffix "Input", this allows the workflow to run with different controls
    eg. Input, H3 and keep results in same dir. However, MACS2 would still over-write the output files from previous run (needs fix).
  • All code should be python3 compatible now
  • Code conforms to PEP8 and this is finally tested on travis-ci

Pit Wiper

• major cleanup and refactoring of wrappers and code structure (but not rules)
• scRNAseq workflow added
• using yaml config files all over, ie.
  1. all wrappers write out a config yaml
  2. Snakefile configuration only depends on provided '--configfile'
• better handling and and more usage of common_functions
• all genome config files converted to yaml, function to load genome information
• own genome file can be provided instead of only pre-configured ones
• paths config file converted to yaml
• eliminate organism specific t2g and symbol files, they are now created by rule from gtf
• check that sleuth is only run if replicates are available
• bugfix: only provided wrapper arguments overwrite either defaults or configfile options, before
  a not provided wrapper option (but in config file provided) would be overwritten by default,
  now there is true hierachy: defaults -> configfile -> wrapper !

v0.4

single-end handling added

v0.3.2.1

0.3.0

• rewrote ChIP-seq workflow completely including wrapper script ChIP-seq
• added histoneHMM for calling broadly enriched regions
• added MACS2 peak quality controls
• revised example.config.yaml files
• moved function get_fragment_length() to common_functions.py
• positional instead of required optional command line arguments
• many small changes
  0.3.1
• run Picard quality control on unfiltered BAM files
• added --gcbias parameter to DNA-mapping wrapper script to run computeGCBias optionally
• replaced --input-dir and --output-dir by --working-dir parameter in ChIP-seq
  wrapper script to specify the working directory, which is output directory of
  the pipeline and must also contain the DNA-mapping pipeline output files
• bugfixes
  0.3.2
• added generation of QC reports for all samples to ChIP-seq pipeline
• added consistency check for ChIP-seq pipeline whether all required input files exist for all samples
• added peak count to MACS2 peak quality controls
  **0.3.2.1 **
• added documentation to README.md
• moved R library

v0.1

• 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