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Commits on Mar 2, 2015

  1. Merge branch 'master' of https://github.com/akahles/icgc_rnaseq_align

    …into akahles-master
    
    Conflicts:
    	Dockerfile
    kellrott committed Mar 2, 2015

Commits on Feb 14, 2015

  1. Added read file whitelisting

    - adapted parsing of metadata table to use current header convention
    - use fastq_files from metadata table for active whitelisting, only
      files that appear in the table will be used for alignment
    - re-organized code a bit to reflect the above changes
    akahles committed Feb 14, 2015

Commits on Feb 9, 2015

  1. adapted SOP version and name

    akahles committed Feb 9, 2015
  2. Changes for the latest version of alignment SOP

    - removed read group parsing from xml and rather use filenames to label
      read groups
    - added memory-limit for BAM sorting
    akahles committed Feb 9, 2015
  3. Implemented new filename convention

    - used analysis ID and aligner name for filename
    - augmented input file by one column to reflect aligner information
    akahles committed Feb 9, 2015
  4. Preparation for v1 uploading

    - bumped STAR version to 2.4.0i in the xml (used for alignments)
    - changed stude name to "PCAWG 2.0"
    akahles committed Feb 9, 2015

Commits on Jan 20, 2015

Commits on Jan 14, 2015

  1. Merge pull request #2 from akahles/master

    STAR alignment wrapper containing 2 pass alignment and use of metadata sheet
    kellrott committed Jan 14, 2015
  2. Changed parameter name for metadata

    Adapted parameter name metaData to metaDataTab as suggested by kellrott.
    akahles committed Jan 14, 2015

Commits on Dec 29, 2014

  1. Added option to use metadata spreadsheet as input.

    - added two new command line options to specify a metadata
      spreadsheet file and an analysis id to align instead of an xml
    - added sanity checks for command line parameters
    - fixed some comments in the code
    akahles committed Dec 29, 2014

Commits on Dec 28, 2014

  1. Implemented 2-pass alignment

    - replaced STAR 2-pass alignment with equivalent workaround until
      2-pass alignment with including annotated junctions is available
    - added option to allow for a weak RG check that replaces that generates
      a generic read group label in case one input file is given but the
      metadata contains several read groups
    - minor changes to in parameter default settings
    akahles committed Dec 28, 2014

Commits on Dec 9, 2014

  1. Merge pull request #1 from akahles/master

    Update to first version of STAR alignment SOP
    kellrott committed Dec 9, 2014

Commits on Dec 4, 2014

  1. Adapted upload specs for STAR

    - adapted STAR version in xml template
    - changed perl script to dynamically fill in run command into xml
    akahles committed Dec 4, 2014
  2. Adapted code to comply with latest header specs

    - add comment line to header
    - add legacy sample ID
    - fix wrong info in some of the fields
    - minor code cleanup
    akahles committed Dec 4, 2014

Commits on Nov 12, 2014

  1. removed absolute path to STAR

    akahles committed Nov 12, 2014

Commits on Nov 11, 2014

  1. Reworked read group logic

    - read group information in header does now support multiple input files
    - improved data management --> data can be written to tmp directory
    - add junctions as output file for two pass run
    - clean up data after STAR run
    - cleaned code from old comment-lines
    akahles committed Nov 11, 2014

Commits on Nov 3, 2014

  1. Extended Dockerfile

    - added bzip
    - added pip to install more python packages
    - added lxml package
    - corrected install of STAR from previous commit
    akahles committed Nov 3, 2014
  2. Adapted python stub to the latest STAR SOP

    - extended and reformatted arg-parser to give users better information
      on the available options
    - added more possibilities to add read group information to the BAM
      header (@rg line) based on direct input or a tcga xml file.
    - replaced downstream usage of samtools with alternatives that are part
      of STAR (sorting, multiple input fast files)
    - allowed alignment of single end read sets
    - added additional decompression setting for bzips
    akahles committed Nov 3, 2014

Commits on Oct 9, 2014

  1. added specific information to the README for running

    Chris Wilks
    Chris Wilks committed Oct 9, 2014

Commits on Oct 8, 2014

  1. updated Dockerfile to include some missing dependencies and added a p…

    …ath var
    Christopher Wilks
    Christopher Wilks committed Oct 8, 2014
  2. added use warnings

    Chris Wilks
    Chris Wilks committed Oct 8, 2014
  3. fixed up some metadata references (e.g. MSKCC instead of UCSC); fixed…

    … path to dump... script
    Chris Wilks
    Chris Wilks committed Oct 8, 2014
  4. updated README to have correct script name

    Christopher Wilks
    Christopher Wilks committed Oct 8, 2014

Commits on Oct 7, 2014

  1. updated script to automatically link the upload file with the PCAWG. …

    …prefix
    Chris Wilks
    Chris Wilks committed Oct 7, 2014
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