ucscCancer / icgc_rnaseq_align
forked from kellrott/icgc_rnaseq_alignmaster
Commits on Mar 2, 2015
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Moving directory to better name
kellrott committedMar 2, 2015 -
Merge branch 'master' of https://github.com/akahles/icgc_rnaseq_align …
…into akahles-master Conflicts: Dockerfile
kellrott committedMar 2, 2015
Commits on Feb 14, 2015
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- 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 committedFeb 14, 2015
Commits on Feb 13, 2015
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replaced metadata headers used in SOP to new consistent header list
akahles committedFeb 13, 2015
Commits on Feb 9, 2015
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adapted filename to meet upload requirements
akahles committedFeb 9, 2015 -
akahles committed
Feb 9, 2015 -
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 committedFeb 9, 2015 -
Implemented new filename convention
- used analysis ID and aligner name for filename - augmented input file by one column to reflect aligner information
akahles committedFeb 9, 2015 -
- bumped STAR version to 2.4.0i in the xml (used for alignments) - changed stude name to "PCAWG 2.0"
akahles committedFeb 9, 2015
Commits on Jan 20, 2015
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Fixing bad dockerfile commit and adding readme
kellrott committedJan 20, 2015
Commits on Jan 15, 2015
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Merging the two docker files for the system build
kellrott committedJan 15, 2015 -
fixed typos in STAR version number
akahles committedJan 15, 2015 -
bumped STAR version from 2.4.0g1 to 2.4.0i1
akahles committedJan 15, 2015
Commits on Jan 14, 2015
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Merge pull request #2 from akahles/master
STAR alignment wrapper containing 2 pass alignment and use of metadata sheet
kellrott committedJan 14, 2015 -
Changed parameter name for metadata
Adapted parameter name metaData to metaDataTab as suggested by kellrott.
akahles committedJan 14, 2015
Commits on Dec 29, 2014
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Updated STAR version to 2.4.0g1
akahles committedDec 29, 2014 -
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 committedDec 29, 2014
Commits on Dec 28, 2014
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- 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 committedDec 28, 2014
Commits on Dec 9, 2014
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Merge pull request #1 from akahles/master
Update to first version of STAR alignment SOP
kellrott committedDec 9, 2014
Commits on Dec 4, 2014
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- adapted STAR version in xml template - changed perl script to dynamically fill in run command into xml
akahles committedDec 4, 2014 -
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 committedDec 4, 2014
Commits on Nov 12, 2014
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akahles committed
Nov 12, 2014
Commits on Nov 11, 2014
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Merge branch 'master' of github.com:akahles/icgc_rnaseq_align
akahles committedNov 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
akahles committedNov 11, 2014
Commits on Nov 3, 2014
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- added bzip - added pip to install more python packages - added lxml package - corrected install of STAR from previous commit
akahles committedNov 3, 2014 -
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 committedNov 3, 2014 -
switched to most recent version of STAR
akahles committedNov 3, 2014
Commits on Oct 9, 2014
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added specific information to the README for running
Chris Wilks committedOct 9, 2014
Commits on Oct 8, 2014
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updated Dockerfile to include some missing dependencies and added a p…
…ath var
Christopher Wilks committedOct 8, 2014 -
Chris Wilks committed
Oct 8, 2014 -
fixed up some metadata references (e.g. MSKCC instead of UCSC); fixed…
… path to dump... script
Chris Wilks committedOct 8, 2014 -
updated README to have correct script name
Christopher Wilks committedOct 8, 2014 -
Adding submission scripts to docker image
kellrott committedOct 8, 2014 -
Working on cghub submit docker image
kellrott committedOct 8, 2014
Commits on Oct 7, 2014
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updated script to automatically link the upload file with the PCAWG. …
…prefix
Chris Wilks committedOct 7, 2014