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Learn More →🚀 Pipelines Team 🚀
27th-29th March 2023
The Hackathon March 2023 Project Board
Slack
#hackathon-march-2023-pipelines
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Learn More →Pipelines Team
Team Purpose
For people:
Team Leads
But always ask first in:
#hackathon-march-2023-pipelines
!Tasks: Devs
Tasks: Volunteers
Remember
Team Members I
Team Members II
Team Members III
Team Members IV
Team Members V
Team Members VI
Team Members VII
Team Members VIII
Reviewing Buddy List
Day One
eager (day 1)
👨👩👦👦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James
eager (day 1) (cont.)
eager (day 1) (cont. 2)
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Learn More →sarek (day 1)
👨👩👦👦: Friederike, Maxime, Matilda, Susanne
proteinfold (day 1)
👨👩👦👦: Athanasios
taxprofiler (day 1)
👨👩👦👦: Sofia, Lili, James
differentialabundance (day 1)
👨👩👦👦: Oskar Wacker, Jonathan Manning, Erika
pangenome (day 1)
👨👩👦👦: Simon
DualRNA-Seq (day 1)
👨👩👦👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota
funcscan (day 1)
👨👩👦👦: Jasmin, Louisa
hgtseq (day 1)
👨👩👦👦: Simone
lightsheetrecon (day 1)
👨👩👦👦: Konrad
magmap (day 1)
👨👩👦👦: Danilo, Emelie, Daniel Lundin
crisprseq (day 1)
👨👩👦👦: Laurence, Júlia
atacseq (day 1)
👨👩👦👦: Björn
new pipeline proposal
bamtofastq (day 1)
👨👩👦👦: SusiJo, Friederike, matrulda
spinningjenny (day 1)
👨👩👦👦: Luca
ensembl sequence pipeline (day 1)
👨👩👦👦: Disha Lodha, Zahra Waheed, Ahmad Zyoud
ensembl genome_prepare pipeline (day 1)
🚧: #16
👨👩👦👦: Disha Lodha, Jorge Alvarez, Lahcen Campbell
COSMIC CMC pipeline (day 1)
👨👩👦👦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Balasz, Helen
🚧: - one group looked at using Docker/Singularity with Nexflow. Working to wrap up our environment inside a container
- Another group worked on how we can use nexflow with the LSF farm
- Another group started creating the nexflow pipeline and wrapping up our first steps.
Aquatic Symbiosis Cobiont Check pipeline (day 1)
👨👩👦👦: Eerik
PhuEgo (day 1)
👨👩👦👦: Haoqi Chen
Nextflow-VEP (day 1)
Nuno Agostinho and Likhitha Surapaneni
pipeline release
quantms
👨👩👦👦: Yasset Perez-Riverol, Julianus Pfeuffer, Sam Minot, Fabian
Day Two
eager (day 2)
👨👩👦👦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James
DualRNA-Seq (day 2)
👨👩👦👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota
pangenome (day 2)
👨👩👦👦: Simon
viralintegration (day 2)
👨👩👦: Alyssa
variantcatalogue (night 1?)
👨👩👦👦: Solenne
Magmap (day 2)
👨👩👦👦: Emelie, Danilo and Daniel
ensembl genome_prepare pipeline (day 2)
🚧: #16
👨👩👦👦: Disha Lodha, Jorge Alvarez, Lahcen Campbell
sammyseq (day 2)
👨👩👦👦: Margherita
spinningjenny (day 2)
sarek (day 2)
👨👩👦👦: Friederike, Maxime, Matilda, Michael, Susanne, Alison
taxprofiler (day 2)
👨👩👦👦: Sofia, Lili, James
nanoseq (day 2)
👨👩👦👦: Chris & Yuk Kei
hgtseq (day 2)
👨👩👦👦: Simone
differentialabundance (day 2)
👨👩👦👦: Jon, Oskar, Erika
proteinfold (day 2)
👨👩👦👦: Athanasios, Leila
funcscan (day 2)
👨👩👦👦: Jasmin
ampliseq (day 2)
👨👩👦👦: Daniel & Daniel
bamtofastq (day 2)
👨👩👦👦: SusiJo, Friederike, matrulda
PhuEgo (day 2)
👨👩👦👦: Haoqi Chen
Nextflow-VEP (day 2)
Nuno Agostinho and Likhitha Surapaneni
Day Three
via GIPHY
Summary today:
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Learn More →via GIPHY
pangenome (day 3)
👨👩👦👦: Simon
variantcatalogue (night 2)
👨👩👦👦: Solenne
viralintegration (day 3)
👨👩👦: Alyssa
metapep (day 3)
👨👩👦👦: Till & Sabrina
spinningjenny (day 3)
👨👩👦👦: Luca
test-dataset
lightsheetrecon (day 3)
👨👩👦👦: Konrad
bamtofastq (day 3)
👨👩👦👦: SusiJo, Friederike, matrulda
magmap (day 3)
👨👩👦👦:
output
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Learn More →sammyseq (day3)
👨👩👦👦: Margherita
PhuEgo (day 3)
👨👩👦👦: Haoqi Chen
Nextflow-VEP (day 3)
Nuno Agostinho and Likhitha Surapaneni
new non nf-core pipelines
via GIPHY
ensembl sequence pipeline (day 3)
👨👩👦👦: Disha Lodha, Zahra Waheed, Ahmad Zyoud - 👀 Modified manifest_stats python script to remove internal Ensembl dependencies - 💻 Created a nextflow module and ran a functional nextflow pipeline! 🎉🎉🎉Aquatic Symbiosis Cobiont Check pipeline (day 2)
👨👩👦👦: Eerik
COSMIC CMC pipeline (day 3)
👨👩👦👦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Helen
🚧: - one group looked at using Docker/Singularity with Nexflow. Working to wrap up our environment inside a container. Progress on containers, nextflow and sqlplus now setup
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Learn More →via GIPHY
DSL2 conversion
DualRNA-Seq (day 3)
👨👩👦👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota
Aquatic Symbiosis Cobiont Check pipeline (day 3)
👨👩👦👦: Eerik
eager (day 3)
People: Selina, Aida Judi, Ian, Thiseas, James
sarek (day 3)
👨👩👦: Friederike, Maxime, Matilda, Michael, Susanne, Alison
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Learn More →exit
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Learn More →viralrecon (day 3)
👨👩👦: Joon
taxprofiler (day 3)
👨👩👦👦: Sofia, Lili, James
proteinfold (day 3)
👨👩👦👦: Athanasios, Leila
ampliseq (day 3)
👨👩👦👦: Daniel & Daniel
funcscan (day 3)
👨👩👦👦: Jasmin
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Learn More →atacseq (day 3)
👨👩👦👦: Björn
rnaseq (day 3)
👨👩👦👦: Harshil?
Just released nf-core/rnaseq v3.11.0
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Learn More →treeval (day 3)
👨👩👦👦: Will Eagles
ensembl genome_prepare pipeline (day 3)
🚧: #16
👨👩👦👦: Disha Lodha, Jorge Alvarez, Lahcen Campbell
COSMIC CMC pipeline (day 3)
👨👩👦👦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Helen
🚧: - More improvement on the Docker container, progress on the singularity container. Investigation integration with Nextflow
- part of Clinvar part of pipeline done in Nextflow, Nextflow can submit some of the processes as LSF jobs.
- Setup of Nexflow Tower almost done
- Part of DN/DS part of the pipeline created in Nextflow
- part of VEP part of the pipeline created in Nexflow, running with LSF for one chromosome. converting a wrapper script into nextflow code.
Summary
- Friederike Hanssen (March 2023)
- Friederike Hanssen (March 2023)
❤️ from James