| 42a7999 | Thanh Lê | 06 April 2020, 09:49:06 UTC | Update environment-illumina.yml (#12) pin ivar to 1.2 | 06 April 2020, 09:49:06 UTC |
| f0ba0a1 | Matt Bull | 03 April 2020, 16:19:57 UTC | Merge branch 'master' of https://github.com/connor-lab/ncov2019-artic-nf | 03 April 2020, 16:19:57 UTC |
| 7b7fa63 | Matt Bull | 03 April 2020, 16:19:32 UTC | Use artic 6-column bedfile instead of our rustically-prepared one | 03 April 2020, 16:19:32 UTC |
| f6cd66b | dkj | 03 April 2020, 15:45:28 UTC | a LEFT primer's name can just contain 'LEFT' (#11) and does not have to end in 'LEFT' Co-authored-by: David K. Jackson <david.jackson@physics.org> | 03 April 2020, 15:45:28 UTC |
| f503400 | Matt Bull | 03 April 2020, 10:40:19 UTC | Round floats and add N% check | 03 April 2020, 10:40:19 UTC |
| 3cd64c1 | Matt Bull | 03 April 2020, 09:58:32 UTC | Increase stringency of QC coverage threshold | 03 April 2020, 09:58:32 UTC |
| fc78b85 | Matt Bull | 02 April 2020, 21:12:47 UTC | Add uncalled base density to QC plots | 02 April 2020, 21:12:47 UTC |
| 333f50b | Matt Bull | 02 April 2020, 15:48:57 UTC | Add depth plots | 02 April 2020, 15:48:57 UTC |
| 14ae215 | Matt Bull | 02 April 2020, 10:42:19 UTC | Move to ivar 1.1 and make ivar variant tsv | 02 April 2020, 10:42:19 UTC |
| e061d26 | Matt Bull | 02 April 2020, 08:52:13 UTC | Make sure n_gaps in qc.py is bookended by start and end | 02 April 2020, 08:52:13 UTC |
| 60623fb | Matt Bull | 02 April 2020, 08:50:36 UTC | Add missing biopython dependency | 02 April 2020, 08:50:36 UTC |
| 93ad8a5 | Matt Bull | 01 April 2020, 21:10:32 UTC | Update README.md | 01 April 2020, 21:10:32 UTC |
| c83750e | Matt Bull | 01 April 2020, 20:32:08 UTC | Add QC filtering of samples to upload, make QC summary csv | 01 April 2020, 20:32:08 UTC |
| ec7bc27 | Matt Bull | 01 April 2020, 14:29:41 UTC | Merge branch 'master' of https://github.com/connor-lab/ncov2019-artic-nf | 01 April 2020, 14:29:41 UTC |
| 4c79dc8 | Liz Batty | 01 April 2020, 11:53:31 UTC | Change zcat to gunzip (#8) | 01 April 2020, 11:53:31 UTC |
| 7986534 | Matt Bull | 01 April 2020, 08:24:01 UTC | Prepares the correct, untrimmed file for upload | 01 April 2020, 08:24:01 UTC |
| 819c86a | Matt Bull | 01 April 2020, 08:19:30 UTC | Refactor upload funtionality | 01 April 2020, 08:19:30 UTC |
| afee872 | Matt Bull | 01 April 2020, 07:45:29 UTC | Merge branch 'master' of https://github.com/connor-lab/ncov2019-artic-nf | 01 April 2020, 07:45:29 UTC |
| 7e9205b | Matt Bull | 01 April 2020, 07:45:15 UTC | Fix use of params.prefix in illumina pipeline | 01 April 2020, 07:45:15 UTC |
| 41729bf | Matt Bull | 01 April 2020, 07:42:39 UTC | Update README.md | 01 April 2020, 07:42:39 UTC |
| 2a9b6d9 | Matt Bull | 01 April 2020, 07:23:40 UTC | Merge pull request #6 from embatty/master Fixes #5 Good catch, thanks. | 01 April 2020, 07:23:40 UTC |
| dc07739 | embatty | 01 April 2020, 04:39:50 UTC | Merge branch 'fix-ivar' | 01 April 2020, 04:39:50 UTC |
| dc45e1e | embatty | 01 April 2020, 04:38:08 UTC | Fix ivar command line options | 01 April 2020, 04:38:08 UTC |
| d28fd0d | Matt Bull | 31 March 2020, 21:29:17 UTC | Remove unneeded params(params). https://github.com/seqeralabs/ncov2019-artic-nf/commit/232b9f27824122c4ebb5e473961e0f84a2ce17cd | 31 March 2020, 21:29:17 UTC |
| 6c853a7 | Matt Bull | 31 March 2020, 20:58:15 UTC | Merge branch 'np-read-group' Support for the new artic workflow | 31 March 2020, 20:58:15 UTC |
| 75c2284 | Matt Bull | 31 March 2020, 20:57:51 UTC | Support revamped artic workflow | 31 March 2020, 20:57:51 UTC |
| 8e1288a | Matt Bull | 30 March 2020, 15:25:38 UTC | Fix environment files to point to fieldbioinformatics@master | 30 March 2020, 15:25:38 UTC |
| 0d576d1 | Matt Bull | 30 March 2020, 15:18:23 UTC | Upload untrimmed BAMs | 30 March 2020, 15:18:23 UTC |
| f36ee3f | Matt Bull | 28 March 2020, 17:13:46 UTC | Inital commits to follow fieldbioinformatics@np-read-group | 28 March 2020, 17:13:46 UTC |
| b07c435 | Matt Bull | 24 March 2020, 14:14:27 UTC | Update README.md | 24 March 2020, 14:14:27 UTC |
| b6201d2 | Matt Bull | 20 March 2020, 13:53:54 UTC | Update nextflow.config Noted here: https://github.com/connor-lab/ncov2019-artic-nf/issues/1#issuecomment-601659266 | 20 March 2020, 13:53:54 UTC |
| 28cab17 | Matt Bull | 20 March 2020, 09:50:06 UTC | Fix recursive fastq searching | 20 March 2020, 09:50:06 UTC |
| 0015370 | Matt Bull | 19 March 2020, 23:38:24 UTC | Add CLIMB upload functionality | 19 March 2020, 23:38:24 UTC |
| 473495a | Matt Bull | 19 March 2020, 19:39:59 UTC | Fix primer trimming output | 19 March 2020, 19:39:59 UTC |
| 9f3f9fa | Matt Bull | 19 March 2020, 19:16:17 UTC | Add an illumina bam/consensus workflow using iVar | 19 March 2020, 19:16:17 UTC |
| 50f561d | Matt Bull | 19 March 2020, 16:15:14 UTC | Make climb_upload directory with correct files | 19 March 2020, 16:15:14 UTC |
| 540a88d | Matt Bull | 19 March 2020, 15:08:47 UTC | Merge illumina work from @tonbar | 19 March 2020, 15:08:47 UTC |
| 71356d4 | Matt Bull | 16 March 2020, 18:45:23 UTC | Fix container build script so that it makes both containers | 16 March 2020, 18:45:23 UTC |
| 895985f | Matt Bull | 15 March 2020, 22:59:58 UTC | Add Medaka pipeline | 15 March 2020, 22:59:58 UTC |
| 5a45300 | Matt Bull | 15 March 2020, 22:59:41 UTC | Better resources configuration | 15 March 2020, 22:59:41 UTC |
| 2b9162f | Matt Bull | 12 March 2020, 22:48:47 UTC | Go back to using symlink to fast5_pass directory | 12 March 2020, 22:48:47 UTC |
| 42b6997 | Matt Bull | 12 March 2020, 22:47:57 UTC | Fix barcoded workflow | 12 March 2020, 22:47:57 UTC |
| daf240f | Matt Bull | 12 March 2020, 12:50:42 UTC | Capture correct group for barcode name | 12 March 2020, 12:50:42 UTC |
| 8e2c6d4 | Matt Bull | 12 March 2020, 10:56:47 UTC | Make linking fast5 files for nanopolish index more flexible | 12 March 2020, 10:56:47 UTC |
| 7d2fc98 | Matt Bull | 12 March 2020, 09:00:28 UTC | Set normalise value in config (artic minion default == 100) | 12 March 2020, 09:00:28 UTC |
| 332fa5e | Matt Bull | 12 March 2020, 08:57:49 UTC | Fix barcoded workflow and change outdir structure slightly | 12 March 2020, 08:57:49 UTC |
| da542ba | Matt Bull | 11 March 2020, 16:11:41 UTC | Fix publishing files from articMinION process | 11 March 2020, 16:11:41 UTC |
| 0e749c9 | Matt Bull | 11 March 2020, 14:56:40 UTC | Fix fast5_pass location for artic minion | 11 March 2020, 14:56:40 UTC |
| cf65020 | Matt Bull | 11 March 2020, 08:35:39 UTC | Fix nanopolish index not using summary | 11 March 2020, 08:35:39 UTC |
| 4e18bf0 | Matt Bull | 10 March 2020, 23:04:01 UTC | Use runPrefix in articMinION process | 10 March 2020, 23:04:01 UTC |
| 9a98d30 | Matt Bull | 10 March 2020, 22:39:07 UTC | Add getRunPrefix function | 10 March 2020, 22:39:07 UTC |
| 007275f | Matt Bull | 10 March 2020, 19:24:10 UTC | Update README.md | 10 March 2020, 19:24:10 UTC |
| 1d077a9 | Matt Bull | 10 March 2020, 19:16:34 UTC | Update README.md | 10 March 2020, 19:16:34 UTC |
| aed4d2e | Matt Bull | 10 March 2020, 18:47:55 UTC | Comment config | 10 March 2020, 18:47:55 UTC |
| 13b14b3 | Matt Bull | 10 March 2020, 18:37:07 UTC | Add SLURM config file and include | 10 March 2020, 18:37:07 UTC |
| 7eb6fb2 | Matt Bull | 10 March 2020, 18:32:12 UTC | Revert to artic repo for fieldbioinformatics | 10 March 2020, 18:32:12 UTC |
| eb92bd0 | Matt Bull | 10 March 2020, 18:26:52 UTC | Inital commit | 10 March 2020, 18:26:52 UTC |
| d9cd992 | Matt Bull | 10 March 2020, 18:20:04 UTC | Initial commit | 10 March 2020, 18:20:04 UTC |
