ONT_pilot_gitlab merge requestshttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests2020-12-08T09:06:33+01:00https://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/78Add zymo workflow2020-12-08T09:06:33+01:00Valentina Galatavalentina.galata@uni.luAdd zymo workflowThe bright futureValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/77Workflow: Zymo - Comparison to Reference Genomes2020-11-06T15:50:07+01:00Susheel BusiWorkflow: Zymo - Comparison to Reference Genomes- added Snakefile to address #83 and #96
- Commit 2578f3d8- added Snakefile to address #83 and #96
- Commit 2578f3d8Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/76Merge "cleanup" branch with "master" branch2020-07-31T14:26:00+02:00Valentina Galatavalentina.galata@uni.luMerge "cleanup" branch with "master" branchMerge `cleanup` with `master`Merge `cleanup` with `master`Clean-upValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/74Fixed assembly annotation rules2020-06-10T07:12:54+02:00Susheel BusiFixed assembly annotation ruleshttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/73updated the mapping rules to include metaspades.bam. Included explicit target...2020-06-09T16:54:10+02:00Susheel Busiupdated the mapping rules to include metaspades.bam. Included explicit target...- updated the mapping rules to include `metaspades.bam`
- Included explicit target in the `assembly_annotation.smk`
- Still missing the `metaspades_mapping` run- updated the mapping rules to include `metaspades.bam`
- Included explicit target in the `assembly_annotation.smk`
- Still missing the `metaspades_mapping` runSusheel BusiSusheel Busihttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/72Merge branch 'master' into 'checkpoint_snakefile'2020-06-09T13:57:46+02:00Valentina Galatavalentina.galata@uni.luMerge branch 'master' into 'checkpoint_snakefile'Master
See merge request susheel.busi/ont_pilot_gitlab!71Master
See merge request susheel.busi/ont_pilot_gitlab!71https://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/71Master2020-06-09T13:57:16+02:00Susheel BusiMaster- merging master to checkpoint_snakefile- merging master to checkpoint_snakefilehttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/70Add latest figure updates2020-06-09T13:44:28+02:00Valentina Galatavalentina.galata@uni.luAdd latest figure updatesWe should add the latest updates from this branch before merging the `master` branch with anything else.We should add the latest updates from this branch before merging the `master` branch with anything else.Manuscript - initial versionValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/69Add PlasFlow and RGI2020-06-03T15:25:13+02:00Valentina Galatavalentina.galata@uni.luAdd PlasFlow and RGImerge `checkpoint_snakefile_VG` into `checkpoint_snakefile` to include `PlasFlow` and `RGI`
**Note**:
The config file and main `snakemake` file have been adjusted.
Further changes should be made in other `snakemake` files as only the fi...merge `checkpoint_snakefile_VG` into `checkpoint_snakefile` to include `PlasFlow` and `RGI`
**Note**:
The config file and main `snakemake` file have been adjusted.
Further changes should be made in other `snakemake` files as only the files for the `analysis` step have been adjusted.
See commits mentioned in the issue #28 and #29.Susheel BusiSusheel Busihttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/68Figures valentina2020-06-04T18:59:29+02:00Susheel BusiFigures valentinahttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/67WIP: Checkpoint snakefile2020-06-09T13:55:55+02:00Susheel BusiWIP: Checkpoint snakefilehttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/66changes for 2019 data2020-05-07T18:41:58+02:00Susheel Busichanges for 2019 datahttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/65updated configs, rules, etc. for 2019_GDB ONT analyses2020-05-06T23:55:24+02:00Susheel Busiupdated configs, rules, etc. for 2019_GDB ONT analyseshttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/64cleaner snakefile for workflow2020-05-01T16:44:47+02:00Susheel Busicleaner snakefile for workflowhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/63Work2020-04-29T17:48:37+02:00Susheel BusiWorkhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/62updated rules2020-04-29T17:46:37+02:00Susheel Busiupdated ruleshttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/61Work2020-04-29T17:44:14+02:00Susheel BusiWorkhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/60updated folder2020-04-29T17:29:28+02:00Susheel Busiupdated folderhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/59Work2020-04-29T17:25:41+02:00Susheel BusiWorkhttps://git-r3lab.uni.lu/ESB/ont_pilot_gitlab/-/merge_requests/58updated workflows_SNAKEFILE, config file, and BINNING rules2020-04-29T17:19:58+02:00Susheel Busiupdated workflows_SNAKEFILE, config file, and BINNING rules