 Jennifer Shelton | 6d0eb75d8b7 | refactor: split chrX calling for Mutect2 on FFPE pairs | | |
Jennifer Shelton | e9b0bc972baM | pull online changesMerge branch 'main' of https://bitbucket.nygenome.org/scm/compbio-internal/templates | | |
Jennifer Shelton | b98bd62406c | fix: use local fastngsadmix ref file | | |
Jennifer Shelton | 6396da53ce6M | Pull changes to mutect2 splits on prem for FFPEMerge branch 'main' of https://bitbucket.nygenome.org/scm/compbio-internal/templates | | |
Jennifer Shelton | 874a22013b7 | feat: increase lancet splits for FFPE runs | | |
Jennifer Shelton | 1ac57b2c31b | feat: increase Mutect2 splits for FFPE runs | | |
Jennifer Shelton | 41343cdad5b | feat: files for splits on HPC with few nodesalso minor changes for new cluster python versions | | |
Jennifer Shelton | 76408668a43 | feat: adding new mutational signature resource files | | |
Jennifer Shelton | d8e13dbb0deM | pulled online changesMerge branch 'main' of https://bitbucket.nygenome.org/scm/compbio-internal/templates into main | | |
Jennifer Shelton | 00b2c37973b | feat: updates | | |
Jennifer Shelton | e66c9993505 | feat: add tcga FASTA files | | |
Jennifer Shelton | 657b1313622 | feat: added updated cosmic files | | |
Jennifer Shelton | ea90ca8dafc | feat: update paths and cosmic file | | |
Jennifer Shelton | e56cd95b751 | feat : minor changes to paths and reports | | |
Jennifer Shelton | 22d6a29fbba | feat: update text | | |
Jennifer Shelton | c95d5f73afeM | feat: add new ann files | | |
Jennifer Shelton | cf68ca56e11 | feat: add draft files | | |
Jennifer Shelton | 39ca9e9f62a | feat: add new refs | | |
Jennifer Shelton | 2ac610013aa | feat: add server report scripts | | |
Jennifer Shelton | 9ee205370a9 | docs: update the tumorId and normalId spelling in docs | | |
Jennifer Shelton | 0bfe2137e3c | docs: update spelling of tumorId and normalId | | |
Jennifer Shelton | dfc74d7386c | fix: update short flag in help | | |
Jennifer Shelton | 90a0a612805 | fix: add analysis group | | |
Jennifer Shelton | 1f303d6722c | feat: add twist interval list | | |
Jennifer Shelton | 7f46d4da99dM | feat: add reduced annotation files | | |
Jennifer Shelton | e1ebe6d0859 | feat: added twist | | |
Jennifer Shelton | 1062dd23355 | feat: added twist | | |
Jennifer Shelton | f3748670638 | feat: run threaded novosort | | |
Jennifer Shelton | 46d5482ec85 | feat: run threaded novosort | | |
Jennifer Shelton | 83f8ed1e475 | feat: add server report | | |
Jennifer Shelton | ba66e5884b2 | feat: fail gracefully when readLength is not provided | | |
Jennifer Shelton | 87a0abbd0cd | fix: track branch using asterisk | | |
Jennifer Shelton | 4beaf5bd3c1M | pull online changes to labelsMerge branch 'main' of https://bitbucket.nygenome.org/scm/compbio-internal/templates into main | | |
Jennifer Shelton | 427d376d617 | feat: add chrX intervals | | |
Jennifer Shelton | 626066d44c1 | docs: update docs | | |
Jennifer Shelton | b8385cf31dc | feat: label with username | | |
Jennifer Shelton | 0dd7490aec8 | feat: overwrite old results | | |
Jennifer Shelton | 770f06081bd | feat: keep filenames unique | | |
Jennifer Shelton | dac857436d5 | fix: minor issue with submissions and update resources | | |
Jennifer Shelton | 4c4cfeb85b3 | feat: add script to load each docker once toavoid error on clusters where docker is pulled too many times
at once in parallel | | |
Jennifer Shelton | 4acfa3aeb82 | feat: handle updates in schema | | |
Jennifer Shelton | cd5ac39c6ac | README.md edited online with Bitbucket | | |
Jennifer Shelton | 39515d4a63c | README.md edited online with Bitbucket | | |
Jennifer Shelton | f4839da9dce | feat: add default labels for tugboat tracking | | |
Jennifer Shelton | 11c230ccf65 | feat: add default labels for tugboat tracking | | |
Jennifer Shelton | 2c10fce697e | feat: add failure messages to the reports unless running in multi mode | | |
Jennifer Shelton | c22b1789ae7 | feat: log failure messages | | |
Jennifer Shelton | beaeb912e10 | feat: log failure messages | | |
Jennifer Shelton | 33b2c854b11 | feat: give full path to runinfo file | | |
Jennifer Shelton | 73ee5e74685 | feat: define all output filenames as flags | | |
