# Hackathon July 2020 --- <!-- Put the link to this slide here so people can follow --> slide: https://hackmd.io/K3knxnbnS8O0vCUbyMR93g --- # Existing pipelines  --- ## Primary focus Developing existing pipelines --- ## Group members - Maxime G. (sarek/rnafusion), Paul C. (sarek), Szilveszter J. (sarek), Friederike H. (sarek) - James F.Y. (eager), Maxime B. (eager), Thiseas L. (eager) - Sabrina K. (mag), Daniel S. (mag) - Leon B. (diaproteomics) - Martin P. (rnafusion) --- ## nf-core/eager James, Alex, Maxime, Thiseas ### Aim - Finishing remaining structural changes and issues before 2.2 release - Finish documentation for 2.2 release - Run benchmarking for 2.2 release --- ### Progress - completed - Simplified BAM filtering parameters [#497](https://github.com/nf-core/eager/issues/497) - Fixed MALT database staging issue [#501](https://github.com/nf-core/eager/issues/501) - Added latest output docs figures and wrote text for remaining tools [#475](https://github.com/nf-core/eager/issues/475) - Bonus: added [tutorial](https://github.com/nf-core/eager/blob/dev/docs/tutorial_profiles.md) on how to use profiles for reproducible science - Considering moving to [nf-co.re](https://nf-co.re) - Test new sequencing configuration merging [#496](https://github.com/nf-core/eager/issues/496) - Updated default dedupper [#508](https://github.com/nf-core/eager/issues/508) - Fixed a bunch of MultiQC stuff [#504](https://github.com/nf-core/eager/issues/504) --- ### Progress - TODO In progress - Benchmarking (starting with comparable pipelines) Pending - Still trying to resolve f\*\*\*ing AWS issues - Write example 'case studies' for usages of pipeline (human, microbiome, pathogen etc.) --- ## nf-core/sarek Maxime, Paul, Szilveszter, Friederike ### Aim - Fixing issues - Updating pipeline - Working on DSL2 --- ### Progress - Create sarek team of core developers on Slack (@sarek-team) and GitHub (@nf-core/sarek) - Fix Control freec restart issue [#229](https://github.com/nf-core/sarek/pull/229) - Add `--ignore_soft_clipped_bases` option for `Mutect2` [#230](https://github.com/nf-core/sarek/pull/230) - Switch to `bwa-mem2` [#237](https://github.com/nf-core/sarek/pull/237) - Fix `Mutect2` typo [#236](https://github.com/nf-core/sarek/pull/236) - "we have progress in sarek, I mean real samples are running with the latest dev and are not failing - yet ;)" - Started re-building sarek with DSL2 starting with figuring out a subworkflow to build all the indices. - Adding variant score recalibration [#89](https://github.com/nf-core/sarek/issues/89): looks the SNP step is working already --- ## nf-core/rnafusion Maxime, Martin ### Aim - Release ### Progress - Release v1.2.0 --- ## nf-core/mag Sabrina, Daniel ### Aim - Fix remaining bugs and prepare release 1.1.0 --- ### Progress Done - Fixed memory conversion issue for SPAdes [#70](https://github.com/nf-core/mag/pull/70) - Compressed assembly files for results [#67](https://github.com/nf-core/mag/pull/67) - Fixed error handlings [#71](https://github.com/nf-core/mag/pull/71), [#71](https://github.com/nf-core/mag/pull/72) - Updated documentation [#75](https://github.com/nf-core/mag/pull/75), [#76](https://github.com/nf-core/mag/pull/76) --- WIP - Remaining issues: - errors due to missing input files (not reproducible) - BUSCO v3: different behaviour for 'scratch = false' and 'scratch = true' - Update to BUSCO v4: basic version running, currently issues with BUSCO databases [#77](https://github.com/nf-core/mag/issues/77) --- ## nf-core/diaproteomics Leon ### Aim - Fix remaining bugs - template update and container update - if time add new processes --- ### Progress - Fixed container building and template update [#17](https://github.com/nf-core/diaproteomics/pull/17) - Added new post processing step DIAlignR [#18](https://github.com/nf-core/diaproteomics/pull/18) - fixed decoding problem in EasyPQP - Future: add EasyPQP step in the pipeline --- ### Wrap up - Cross environment commnication - A small library to solve messaging pain - TypeScript Rocks :tada: --- ### Thank you! :sheep: