| Age | Commit message (Expand) | Author |
|---|
| 2018-12-11 | qsub: prefix directories to prevent cleanup deleting top level dir | Justin Bedo |
| 2018-12-10 | gridss: add java heapSize arguments. | l-d-s |
| 2018-12-10 | qsub: fix $TMPDIR location | Justin Bedo |
| 2018-12-10 | bowtie: init | Justin Bedo |
| 2018-12-10 | gridss: fix tmpdir bug. | l-d-s |
| 2018-12-06 | gridss: remove redundant collectGridssMetrics | l-d-s |
| 2018-11-29 | Correct argument for gridss option file | l-d-s |
| 2018-11-29 | gridss: fix for nix installations outside of /nix | Justin Bedo |
| 2018-11-29 | Revert "test-tnpair: avoid gridss.call while it's broken" | l-d-s |
| 2018-11-27 | Add licence | Justin Bedo |
| 2018-11-27 | Expand README and add simple example pipeline | Justin Bedo |
| 2018-11-26 | qsub: output non-retryable errors | Justin Bedo |
| 2018-11-26 | qsub: let sleep timing be configurable | Justin Bedo |
| 2018-11-26 | qsub: retry qsub if requested | Justin Bedo |
| 2018-11-26 | Merge branch 'master' of https://github.com/PapenfussLab/bionix | l-d-s |
| 2018-11-26 | Also need config for 'assemble' step. | l-d-s |
| 2018-11-23 | qsub: update to check job_state field | Justin Bedo |
| 2018-11-23 | qsub: be more specific with qstat polling | Justin Bedo |
| 2018-11-22 | Merge branch 'master' of https://github.com/PapenfussLab/bionix | l-d-s |
| 2018-11-22 | gridss: restructure gridss pipeline | Justin Bedo |
| 2018-11-22 | samtools-sort: handle missing 'none' sorting case | Justin Bedo |
| 2018-11-22 | gridss: fix configure file optional string error | Justin Bedo |
| 2018-11-20 | Add some typed fetchurl functions | Justin Bedo |
| 2018-11-15 | Fix up gridss config file. | l-d-s |
| 2018-11-15 | test-tnpair: avoid gridss.call while it's broken | l-d-s |
| 2018-11-15 | gridss.softClipsToSplitReads: sort -> sorting | l-d-s |
| 2018-11-15 | Syntax. | l-d-s |
| 2018-11-15 | Ignore temporary files. | l-d-s |
| 2018-11-15 | Need to test config != null | l-d-s |
| 2018-11-15 | Merge branch 'master' of https://github.com/PapenfussLab/bionix | l-d-s |
| 2018-11-15 | Ignore .DS_Store | l-d-s |
| 2018-11-15 | gridss.softClipsToSplitReads: sort ordering is not preserved | Justin Bedo |
| 2018-11-14 | Add ensembl mouse transcriptome | Justin Bedo |
| 2018-11-13 | Merge branch 'master' of https://github.com/PapenfussLab/bionix | l-d-s |
| 2018-11-12 | Attempt to integrate config file into GRIDSS stage | l-d-s |
| 2018-11-12 | Function to great ini-style gridss config file. | l-d-s |
| 2018-11-07 | Fix to gridss. | l-d-s |
| 2018-11-07 | Add bwa to softClipsToSplitReads | l-d-s |
| 2018-11-02 | Allow bwa-mem to take gzipped fastq inputs | Justin Bedo |
| 2018-11-02 | kallisto: init | Justin Bedo |
| 2018-11-01 | samtools-sort: don't sort if already sorted | Justin Bedo |
| 2018-10-29 | Split gridss into constituents | Justin Bedo |
| 2018-10-29 | bwa-mem: BWA output is query name sorted | Justin Bedo |
| 2018-10-29 | init: samtools-markdup | Justin Bedo |
| 2018-10-29 | init: samtools-fixmate | Justin Bedo |
| 2018-10-26 | init: mutect | Justin Bedo |
| 2018-10-26 | init: samtools-dict | Justin Bedo |
| 2018-10-26 | init: cosmic & dbsnp for grch38 | Justin Bedo |
| 2018-10-25 | Improve type safety of samtools-merge | Justin Bedo |
| 2018-10-25 | Simplify types for sorting | Justin Bedo |
