| 8af5152 | Matt Bull | 08 April 2021, 15:56:30 UTC | Fix params.gff undefined and remove CLIMB upload (#99) * Fix gff undefined * Remove CLIMB upload automation * Remove CLIMB config * Add back collateSamples process * Fix import of missing upload workflow | 08 April 2021, 15:56:30 UTC |
| c860345 | Dan Fornika | 08 April 2021, 14:16:01 UTC | Handle variants with consequence type 'stop_retained' (#91) | 08 April 2021, 14:16:01 UTC |
| 9ac3119 | Matt Bull | 23 December 2020, 17:36:52 UTC | Add ability to type sequences by their variants (#83) * Add script to type variants and consequences * Update deps for typing script * Rename type_variants.py so its not confused with AR group tool * Add NF processes for typing and making summary csvs * Add example yaml and gff files for typing * Add a typing workflow that can be attached to nanopore or illumina data * Update config options for typing * Update conda deps for typing script * Add typing workflow to illumina pipeline * Add named outputs to typing process and update workflow * Add typing workflow to nanopore pipeline * Update help with new options * Tidy up commented line in qc.nf * Make output of typing csvs optional for when no variants pass filters * Output boxplots from nanopore pipeline * Add rudimentary tests of typing code * Add N501Y.V2 variants to types.yaml because why not * Add comments to example typing.yaml file | 23 December 2020, 17:36:52 UTC |
| 1f74eff | Matt Bull | 18 November 2020, 14:59:49 UTC | Ivar 1.3 (#81) * Update ivar version to 1.3 * Pin artic version to 1.1.3 * Test against v1.1.1 * Remove depth plot png files from tests | 18 November 2020, 14:59:49 UTC |
| af2e515 | Matt Bull | 07 October 2020, 10:35:17 UTC | Create LICENSE | 07 October 2020, 10:35:17 UTC |
| d613e9d | Matt Bull | 26 September 2020, 20:45:26 UTC | Fix BAM header cleaning (#78) * Fix samtools sort reversion * Move BAM header cleaning to trimPrimerSequences process | 26 September 2020, 20:45:26 UTC |
| db1b21b | Matt Bull | 25 September 2020, 11:24:19 UTC | Switch to multistage builds for Docker and Singularity (#77) | 25 September 2020, 11:24:19 UTC |
| 9267579 | Matt Bull | 24 September 2020, 19:31:48 UTC | Fix up how samples are searched for using fileglobs (#76) * Move fastq globbing into a module and join paths properly * Use makeFastqSearchPath to make fileglobpath in main.nf * Add PHW specific config for sample names * Restore test against previous release * Sometimes paths have a trailing slash or two, remove | 24 September 2020, 19:31:48 UTC |
| 161edf7 | Matt Bull | 24 September 2020, 16:06:33 UTC | Clean bam headers (#75) * Add cleanBamHeader flag * Add optional scripts for using cleanBamHeader flag | 24 September 2020, 16:06:33 UTC |
| 1eed11b | Matt Bull | 15 September 2020, 16:54:28 UTC | Add new option to remove samples with low reads after guppyplex (#74) | 15 September 2020, 16:54:28 UTC |
| e77feed | Matt Bull | 09 September 2020, 09:15:01 UTC | Nanopore tests (#69) * Fix primer scheme paths after ARTIC update * Add nanopore pipeline tests * Fix nanopore tests and cleanup * Fix sneaky null in nanopore workflow, yay tests * Fix path to nanopore test script | 09 September 2020, 09:15:01 UTC |
| 02af8e0 | Matt Bull | 09 September 2020, 08:16:06 UTC | Fix primer scheme paths after ARTIC update (#68) | 09 September 2020, 08:16:06 UTC |
| bc9884d | FredDodd6 | 08 September 2020, 16:31:41 UTC | updating ivar version to 1.2.3 (#66) * updating ivar version to 1.2.3 * fixing samtools version to v1.10 to allow conda to solve the environment * Fix build script stamped on by force-push * Fix conda samtools dependency issue * Switch to mamba for dependency resolution - fast! * Turn of NXF ANSI logging * Update primer scheme URLs for Artic * Can't test against previous release, ARTIC changes scheme repo * Previous release doesn't even work anymore - ARTIC repo changed * Later tests depend on test_PR_against_release - reinstate Co-authored-by: Matt Bull <matthew.bull@wales.nhs.uk> | 08 September 2020, 16:31:41 UTC |
| 2391185 | Matt Bull | 26 August 2020, 14:49:23 UTC | Update tests to latest commit | 26 August 2020, 14:49:23 UTC |
| 307b094 | Matt Bull | 26 August 2020, 14:34:42 UTC | Set default illuminaKeepLen = 30 (#64) * Set default illuminaKeepLen = 30 Work from @tonbar shows this is appropriate and beneficial to tagmented libraries, @dkj and co show same for ligated libraries so makes sense to change default. * Fix tests to succeed | 26 August 2020, 14:34:42 UTC |
| 33b0f4c | Matt Bull | 24 July 2020, 16:32:56 UTC | Remove mpileup depth limit by default (#63) | 24 July 2020, 16:32:56 UTC |
| 84a7abe | Shriram Bhosle | 24 July 2020, 12:26:40 UTC | Feature/update bam to cram (#62) * updated samtools version to 1.10 to enable indexing in a single command * updated samtools command to output index in a single command * bam to cram conversion now enabled for all bam files including qc failed * corrected typo * removed artefacts created during test * updated all conda to latest * reverted changes from in the Docker and Singularity environments * updated samtools v1.10-0 and command in bamToCram to output bam index in a single command bam to cram conversion now enabled for all bam files including qc failed * Remove mpileup depth limit in consensus generation (#51) The current samtools depth reduction technique is not suitable for the high depth NovaSeq output together with end of amplicon (ligated/tailed) adapters. * Update ivar consensus calling mpileup command (#54) * Update ivar consensus calling mpileup command Updated ivar documentation to adds `-aa` to `samtools mpileup` here: https://github.com/andersen-lab/ivar/blob/master/docs/MANUAL.md. cc @jts * Move to Miniconda3 for tests * Fix PR test script and temp allow tests to complete * Update tests to compare against 5e00ba9 (#55) * Qc update (#56) * Update qc.py to reflect changed standards * Filter out Illumina Undetermined_S0 * Make sure to negate the matcher * Add minReadsPerBarcode parameter for Nanopore workflow (#57) The barcode<n*> directories of de-plexed Fastq input are filtered to exclude any containing fewer than 5 files (guppy makes all of the barcode directories, whether you used the barcodes or not). This patch changes the filter to scan the files and count the records within to 1) avoid excluding barcodes where many reads are in fewer than 5 files and 2) avoid including barcodes where there are very few reads in more than 5 files. This threshold can be changed with the new optional parameter minReadsPerBarcode, which defaults to 100 reads. Co-authored-by: Keith James <dev@deoxybyte.co.uk> * Remove unnecessary samtools view -bS (#48) Co-authored-by: ac55-sanger <ac55@github.com> * use ivar default of 30 for illuminaKeepLen, and comment (#61) Co-authored-by: David K. Jackson <david.jackson@physics.org> * pulled chnages from upstream master to run tests successfully Co-authored-by: dkj <david.jackson@sanger.ac.uk> Co-authored-by: Matt Bull <bullmj2@gmail.com> Co-authored-by: Keith James <47220353+kjsanger@users.noreply.github.com> Co-authored-by: Keith James <dev@deoxybyte.co.uk> Co-authored-by: Ashwini Chhipa <58439277+ac55-sanger@users.noreply.github.com> Co-authored-by: ac55-sanger <ac55@github.com> Co-authored-by: David K. Jackson <david.jackson@physics.org> | 24 July 2020, 12:26:40 UTC |
| 5321844 | dkj | 07 July 2020, 13:22:52 UTC | use ivar default of 30 for illuminaKeepLen, and comment (#61) Co-authored-by: David K. Jackson <david.jackson@physics.org> | 07 July 2020, 13:22:52 UTC |
| a6fe2cd | nodrogluap | 07 July 2020, 13:20:54 UTC | Added libxcb, default Qt library backend for graphics rendering, to dependencies (#60) | 07 July 2020, 13:20:54 UTC |
| e4256ea | Ashwini Chhipa | 30 June 2020, 14:23:34 UTC | Remove unnecessary samtools view -bS (#48) Co-authored-by: ac55-sanger <ac55@github.com> | 30 June 2020, 14:23:34 UTC |
| 7bc778f | Keith James | 30 June 2020, 14:22:57 UTC | Add minReadsPerBarcode parameter for Nanopore workflow (#57) The barcode<n*> directories of de-plexed Fastq input are filtered to exclude any containing fewer than 5 files (guppy makes all of the barcode directories, whether you used the barcodes or not). This patch changes the filter to scan the files and count the records within to 1) avoid excluding barcodes where many reads are in fewer than 5 files and 2) avoid including barcodes where there are very few reads in more than 5 files. This threshold can be changed with the new optional parameter minReadsPerBarcode, which defaults to 100 reads. Co-authored-by: Keith James <dev@deoxybyte.co.uk> | 30 June 2020, 14:22:57 UTC |
| fdd4c1e | Matt Bull | 25 June 2020, 08:40:10 UTC | Qc update (#56) * Update qc.py to reflect changed standards * Filter out Illumina Undetermined_S0 * Make sure to negate the matcher | 25 June 2020, 08:40:10 UTC |
| 9a91994 | Matt Bull | 22 June 2020, 18:12:05 UTC | Update tests to compare against 5e00ba9 (#55) | 22 June 2020, 18:12:05 UTC |
| 5e00ba9 | Matt Bull | 22 June 2020, 17:35:12 UTC | Update ivar consensus calling mpileup command (#54) * Update ivar consensus calling mpileup command Updated ivar documentation to adds `-aa` to `samtools mpileup` here: https://github.com/andersen-lab/ivar/blob/master/docs/MANUAL.md. cc @jts * Move to Miniconda3 for tests * Fix PR test script and temp allow tests to complete | 22 June 2020, 17:35:12 UTC |
| d0fd43c | dkj | 17 June 2020, 11:16:00 UTC | Remove mpileup depth limit in consensus generation (#51) The current samtools depth reduction technique is not suitable for the high depth NovaSeq output together with end of amplicon (ligated/tailed) adapters. | 17 June 2020, 11:16:00 UTC |
| d5647aa | Matt Bull | 05 June 2020, 11:24:46 UTC | Add help message and fix nanopore conda env for singularity (#50) | 05 June 2020, 11:24:46 UTC |
| b3e0859 | Shriram Bhosle | 26 May 2020, 17:39:49 UTC | Feature/sb43 bam to cram (#45) * feature: bamToCram function to generate reference embeded cram and crai output from qc passed BAM files added outCram parameter to illumina conf file added cramOut user paramter in config files, implemented cram generation only for qc-passed bam files added test file and updated pull_request.yml updated README with outCram option added qc passing test subsample2, removed previous unit test files added fastq test data using subsample2.cram file * feature: bamToCram function to generate reference embedded cram and crai output from qc passed BAM files added outCram parameter to illumina conf file added cramOut user paramter in config files, implemented cram generation only for qc-passed bam files added test file and updated pull_request.yml updated README with outCram option added qc passing test subsample2, removed previous unit test files added fastq test data using subsample2.cram file | 26 May 2020, 17:39:49 UTC |
| 8b0f5ea | Matt Bull | 26 May 2020, 17:38:59 UTC | Use artic package directly from conda | 26 May 2020, 17:38:59 UTC |
| 48816ee | Sendu Bala | 06 May 2020, 13:26:03 UTC | Allow --ref option to be a symlink. (#44) * Allow --ref option to be a symlink. * Correct test for symlinked ref. | 06 May 2020, 13:26:03 UTC |
| 2f7ae82 | mgcam | 04 May 2020, 10:47:23 UTC | add number of primer trimmed aligned reads to QC summary (#43) | 04 May 2020, 10:47:23 UTC |
| b88235d | Sendu Bala | 30 April 2020, 13:00:20 UTC | Fix #40: let extras.yml be found from anywhere. (#41) * Fix #40: let extras.yml be found from anywhere. * Change conda tests to test from outside repo dir. * Correct location of artifacts. * Debug PWD. | 30 April 2020, 13:00:20 UTC |
| c4c617b | Matt Bull | 27 April 2020, 08:26:03 UTC | Conda env tracking (#39) * Update conda env from artic-ncov2019 on the fly * Update containers to pull unified conda env from artic-ncov2019 * Add curl to Nanopore Singularity image * Refactor Docker/Singularity/Conda config * Make Conda env file for QC process * Use conda update to add QC env file to container images * Fix conda versions in illumina environment * Update Conda cache test with new environment.yml path | 27 April 2020, 08:26:03 UTC |
| d31e8ef | Matt Bull | 26 April 2020, 12:24:24 UTC | Use file() in Nanopore barcode detection to (hopefully) support cloud storage (#37) | 26 April 2020, 12:24:24 UTC |
| 668ce73 | Sendu Bala | 26 April 2020, 10:41:55 UTC | Add github ci test workflow, scripts and data. (#35) Co-authored-by: gn5 <gn5@sanger.ac.uk> | 26 April 2020, 10:41:55 UTC |
| 39bd871 | Thanh Lê | 21 April 2020, 14:42:29 UTC | update regex search for nanoporeBarcodeDirs (#34) update regex search for nanoporeBarcodeDirs so it can detect: barcode1 barcode01 barcode001 barcode0001 | 21 April 2020, 14:42:29 UTC |
| 6feedcd | Matt Bull | 15 April 2020, 15:05:52 UTC | Revert to writing directly to output for QCCSV, no publishing | 15 April 2020, 15:05:52 UTC |
| ca4c41d | Matt Bull | 15 April 2020, 14:32:37 UTC | Use Nextflow file, not Java File in QCCSV process | 15 April 2020, 14:32:37 UTC |
| 8756842 | Matt Bull | 15 April 2020, 09:20:35 UTC | Fix QCCSV process writing outside task.workDir | 15 April 2020, 09:20:35 UTC |
| dd5cb06 | Matt Bull | 14 April 2020, 17:45:20 UTC | Pin fieldbioinformatics version to commit | 14 April 2020, 17:45:20 UTC |
| 505304d | Matt Bull | 10 April 2020, 11:53:00 UTC | Fix medaka fast5 hard requirement | 10 April 2020, 11:53:00 UTC |
| cf01166 | Sendu Bala | 08 April 2020, 10:16:09 UTC | Add Sanger config (#23) * Add Sanger-specific config, moving some from lsf.config. * Include COG-UK config last, so they override. * Define largecpu. * Remove unused config files. * Update Executors help now there are institutional configs. * Revert inclusion of largemem definition. * Fix braces broken by 37a3f50. | 08 April 2020, 10:16:09 UTC |
| 37a3f50 | mikek498 | 07 April 2020, 20:39:26 UTC | Added Google Life Sciences config (#24) * Adds support for Google Cloud Life Sciences API * fixed gls config * Update gls.config | 07 April 2020, 20:39:26 UTC |
| e6a8695 | Thanh Lê | 07 April 2020, 20:37:20 UTC | update profile (#26) | 07 April 2020, 20:37:20 UTC |
| 0015ce5 | Matt Bull | 07 April 2020, 12:25:48 UTC | Remove all resources config from general config files | 07 April 2020, 12:25:48 UTC |
| 0400879 | Matt Bull | 07 April 2020, 12:23:58 UTC | Add model for COG-UK institutions to set profiles | 07 April 2020, 12:23:58 UTC |
| 7ca7a33 | Sendu Bala | 07 April 2020, 09:08:32 UTC | Fix prepareReferenceFiles to work when ref not supplied. (#19) | 07 April 2020, 09:08:32 UTC |
| e487e75 | Matt Bull | 06 April 2020, 22:03:29 UTC | Refactor local reference and bedfile preparation into separate workflow | 06 April 2020, 22:03:29 UTC |
| fbf1c60 | Matt Bull | 06 April 2020, 21:50:21 UTC | Fix indentation error | 06 April 2020, 21:50:21 UTC |
| 1b494e6 | mgcam | 06 April 2020, 19:05:36 UTC | shortcut in qc outcome evaluation for empty fasta, which helps (#18) to avoid division by zero run time error | 06 April 2020, 19:05:36 UTC |
| f71e74b | Sendu Bala | 06 April 2020, 16:16:44 UTC | Allow use of local scheme files (#16) * Resolve isssue #11 - use local schemeRepoURL. * Resolve #14 - provide ivar bed and indexed ref file. New ivarBed and alignerRefPrefix config options. Indexing split out of readMapping process in to indexReference process. Specify previously added cram config option in config file. * Check validity of ivarBed and alignerRefPrefix option usage. * Fix usage of articDownloadScheme, which changed upstream. * Fix following changes upstream. * Move illumina-only options to illumina config file. * Check that ivarBed is supplied when alignerRefPrefix is. * Fix cherrypick mistakes. * Document use of ivarBed and alignerRefPrefix. | 06 April 2020, 16:16:44 UTC |
| 01da882 | Matt Bull | 06 April 2020, 15:47:23 UTC | Clean up cram channel and cram -> fastq process | 06 April 2020, 15:47:23 UTC |
| dc838fb | Sendu Bala | 06 April 2020, 15:00:16 UTC | Add cram input option for illumina workflow (#14) * Resolved issue #3 - integrate cram to fastq conversion step * Added missing include. Fixed copy/paste error * Corrected another copy/paste error * Added missing qoutes from output tuple * Fix --cram mode following upstream changes. * Define cram option in config. * Document new --cram flag. Co-authored-by: Jon Keatley <jk23@sanger.ac.uk> | 06 April 2020, 15:00:16 UTC |
| cae2c3e | Sendu Bala | 06 April 2020, 12:50:10 UTC | New lsf profile (#15) * solves #1 * Document new -lsf profile. Co-authored-by: Roberto Amato <ra4@sanger.ac.uk> | 06 April 2020, 12:50:10 UTC |
| 89e784d | Sendu Bala | 06 April 2020, 12:27:34 UTC | New --cache option (#13) * Add --cache option. * Add comment to explain --cache. * Document new --cache flag. | 06 April 2020, 12:27:34 UTC |
| 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 |
