source: other/pipeline

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Diff Rev Age Author Log Message
(edit) @5934   2 years Nicklas Nordborg References #1243: Improve status checking for NovaSeq? Updated the …
(edit) @5856   2 years Nicklas Nordborg References #1231: Add support for sequencing with NovaSeq? Added …
(edit) @5842   2 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for …
(edit) @5840   2 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for …
(edit) @5838   2 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for the …
(edit) @5836   2 years Nicklas Nordborg References #1218: Implement MIPs alignment Added functions for …
(edit) @5834   2 years Nicklas Nordborg References #1218: Implement MIPs alignment Started to implement a …
(edit) @5825   3 years Jari Häkkinen Change needed to find R's BLAS/LAPACK implementation
(edit) @5810   3 years Nicklas Nordborg References #1222: Remove the G5 distance calculations from the variant …
(edit) @5807   3 years Nicklas Nordborg References #1215: Include mutation signature analysis in the variant …
(edit) @5796   3 years Nicklas Nordborg References #1215: Include mutation signature analysis in the variant …
(edit) @5771   3 years Nicklas Nordborg References #1208: Implement wizard for building database of variant …
(edit) @5769   3 years Nicklas Nordborg References #1208: Implement wizard for building database of variant …
(edit) @5767   3 years Nicklas Nordborg References #1208: Implement wizard for building database of variant …
(edit) @5753   3 years Nicklas Nordborg References #1205: Variant calling fails with "malformed BED entry" …
(edit) @5747   3 years Nicklas Nordborg Fixes an issue with missing "N" values in the lookup tables for GC …
(edit) @5719   3 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added …
(edit) @5718   3 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Helper script …
(edit) @5712   3 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added helper …
(edit) @5709   3 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added python …
(edit) @5698   3 years Nicklas Nordborg References #1199: Implement Variant calling pipeline Added wrapper …
(edit) @5610   3 years Jari Häkkinen removed obsolete script
(edit) @5589   3 years Nicklas Nordborg References #1146: Demux for the MIPs pipeline Added fqpaste.pl to the …
(edit) @5529   3 years Nicklas Nordborg References #1161: Update picard to 2.20 Adding the picard2 wrapper …
(edit) @5476   3 years Nicklas Nordborg References #1142: Create MIPs flow cell and start sequencing Updated …
(edit) @5474   3 years Nicklas Nordborg References #1142: Create MIPs flow cell and start sequencing Added a …
(edit) @4589   5 years Nicklas Nordborg References #997: Implement new secondary analysis pipeline Updated …
(edit) @4566   5 years Nicklas Nordborg References #983: Merge the Tophat alignment and Cufflinks job to a …
(edit) @4045   6 years Nicklas Nordborg References #901: Set multiple paths for run-archive Updated the …
(edit) @3698   7 years Nicklas Nordborg Adding nextseq_status.sh script for checking the status of a NextSeq?
(edit) @3589   7 years Jari Häkkinen Restoring svn:eol-style to LF
(edit) @3586   7 years Jari Häkkinen Fixing svn:eol-style
(edit) @3585   7 years Jari Häkkinen Updating post-alingment script to latest released version. The script …
(edit) @3584   7 years Jari Häkkinen Fixing svndigest&svncopyright properties
(edit) @3583   7 years Jari Häkkinen Fixing Id keyword
(edit) @3099   8 years Nicklas Nordborg Updating Picard wrapper script to make it compatible with Picard 1.128 …
(edit) @2852   8 years Nicklas Nordborg Ignore .project file from Eclipse.
(edit) @2831   8 years Jari Häkkinen New version from Christian. added proper argument/option handling; …
(edit) @2830   8 years Jari Häkkinen Print integers as integers.
(edit) @2786   8 years Nicklas Nordborg References #653: Use explicit paths to all important program used in …
(edit) @2749   8 years Nicklas Nordborg Adding script for replacing tracking_id values in the fpkm_tracking …
(edit) @2696   8 years Nicklas Nordborg Adding script for fixing the unmapped.bam file generated by tophat so …
(edit) @2679   8 years Nicklas Nordborg Adding script for calculating average of fragment lengths.
(edit) @2567   8 years Nicklas Nordborg Removing scripts that are no longer used by reggie.
(edit) @2558   8 years Nicklas Nordborg Forgot to execute the last samtools command
(edit) @2557   8 years Nicklas Nordborg Added 'alignment_statisics.sh' which replaces the …
(edit) @2537   8 years Nicklas Nordborg Adding wrapper script for directing output to stderr or stdout …
(edit) @2496   8 years Nicklas Nordborg Adding svn properties
(edit) @2495   8 years Nicklas Nordborg Adding wrapper for calling trimmomatic. Includes default settings for …
(edit) @2442   8 years Nicklas Nordborg Check enironment variable PicardMemory? for amount of memory to give to …
(edit) @2430   8 years Nicklas Nordborg Switched from illumina2bam_wrapper to picard for demultiplexing. …
(edit) @2421   8 years Nicklas Nordborg Renamed the 'filtered' step to 'masked'. See …
(edit) @2413   8 years Nicklas Nordborg Remove 'filter_' prefix in the PE_filter script.
(edit) @2398   8 years Nicklas Nordborg Adding statistics_tophat.sh
(edit) @2396   8 years Nicklas Nordborg Adding tophat_single.sh and sync_resyltfiles.sh scrips. tophat_single …
(edit) @2393   8 years Nicklas Nordborg Adding PE_filter.sh script. Changes from original script is that …
(edit) @2387   8 years Nicklas Nordborg Scripts used for the demux and merge steps in reggie.
(edit) @2383   8 years Nicklas Nordborg Creating trunk and tags folder for the pipeline project.
(add) @2382   8 years Nicklas Nordborg Creating root folder for the 'pipeline' scripts.
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