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Hackathon March 2021
Pipelines group
Group Members
Sarek 3.0 - Achievements
Monday
Tuesday
Wednesday
scRNAseq - Achievements
Monday
Tuesday
Wednesday
Hlatyping - Achievements
Monday
Please chat on #hlatyping in Slack if possible. Alex will be around there and hopefully start working on it Monday afternoon :-)
Tuesday
Wednesday
- The image file may be corrupted
- The server hosting the image is unavailable
- The image path is incorrect
- The image format is not supported
Learn More →Methylseq - Achievements
Monday
Tuesday
Patrick: preparing nf-core/methylseq for 1.6 release (hopefully the last dsl1 release)
Patrick: working on dsl2 port
21.03.0-edge
; needs more investigationUnable to make field private static volatile java.util.List java.nio.file.spi.FileSystemProvider.installedProviders accessible: module java.base does not "opens java.nio.file.spi" to unnamed module @71d44a3
-> nextflow reinstalled solved itWednesday
Pangenome - Achievements
Monday
nextflow_schema.json
up to date https://github.com/nf-core/pangenome/pull/58.Tuesday
Wednesday
Ampliseq - Achievements
Monday
Tuesday
Wednesday
Bactmap - Achievements
Monday
Tuesday
next step to contribute other missing modules and stitch them together
Wednesday
Bcellmagic - Achievements
Monday
@ggabernet template update to v1.13.1
@ssnn is working in a temp private repo on some modules for bcellmagic. Template upgrade done. Working now on DSL2 regorganization (modules, params, doc…)
Tuesday
@ggabernet Fixing a couple of issues for DSL2 release
@ssnn Figured out how to reorganize the code, and use custom container.
Eager - Achievements
Monday
Tuesday
Wednesday
mag - Achievements
Monday
Tuesday
Wednesday
DIAproteomics / MHCquant - Achievements
Monday
[Leon] Template update merge conflicts resolved
[Leon] Opened two PRs:
couple of bugs remain after merging
Tuesday
[Leon] Found an issue in the 1.13.1 template (https://github.com/nf-core/tools/issues/937)
[Kevin M and Phil E] Solved the issue
[Leon] Two PRs still open but:
[Leon] + added an review for:
Wednesday
crisprquant - Achievements
Monday
Tuesday
Wednesday
circrna - Achievements
Monday
Tuesday
--bsj_reads
allowing users to filter by minimum circRNA reads counts.--tool_filter
allowing users to take union/intersection of mutliple quantification tools.Wednesday
--tool_filter
to take integers instead of strings (i.e output circrnas must be called by at least n tools)@BarryDigby
Thank you Gisela for leading this workgroup :)