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Commits on Nov 03, 2014
- 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
- added bzip - added pip to install more python packages - added lxml package - corrected install of STAR from previous commit
Commits on Nov 11, 2014
- 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
Commits on Nov 12, 2014
Commits on Dec 04, 2014
- add comment line to header - add legacy sample ID - fix wrong info in some of the fields - minor code cleanup
- adapted STAR version in xml template - changed perl script to dynamically fill in run command into xml
Commits on Dec 09, 2014
Update to first version of STAR alignment SOP
Commits on Dec 28, 2014
- 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
Commits on Dec 29, 2014
- 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
Commits on Jan 14, 2015
Adapted parameter name metaData to metaDataTab as suggested by kellrott.
STAR alignment wrapper containing 2 pass alignment and use of metadata sheet
Commits on Jan 15, 2015
Commits on Jan 20, 2015
Commits on Feb 09, 2015
- bumped STAR version to 2.4.0i in the xml (used for alignments) - changed stude name to "PCAWG 2.0"
- used analysis ID and aligner name for filename - augmented input file by one column to reflect aligner information
- removed read group parsing from xml and rather use filenames to label read groups - added memory-limit for BAM sorting
Commits on Feb 13, 2015
Commits on Feb 14, 2015
- 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
Commits on Mar 02, 2015
…into akahles-master Conflicts: Dockerfile
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