| HEAD | 8af5152 | 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 |
| refs/heads/illumina | aaba142 | dockerfile created | 28 April 2020, 17:54:17 UTC |
| refs/heads/master | 8af5152 | 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 |
| refs/heads/variant_definitions | 7d57d24 | Add --medaka_model to tests | 09 April 2021, 17:55:34 UTC |
| refs/tags/v1.0.0 | 1eed11b | Add new option to remove samples with low reads after guppyplex (#74) | 15 September 2020, 16:54:28 UTC |
| refs/tags/v1.1.0 | 9267579 | 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 |
| refs/tags/v1.1.1 | d613e9d | Fix BAM header cleaning (#78) * Fix samtools sort reversion * Move BAM header cleaning to trimPrimerSequences process | 26 September 2020, 20:45:26 UTC |
| refs/tags/v1.2.0 | 1f74eff | 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 |
| refs/tags/v1.3.0 | 9ac3119 | 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 |
