cfusterot / multisap Goto Github PK
View Code? Open in Web Editor NEWMultiome Sequencing Analysis Pipeline
License: MIT License
Multiome Sequencing Analysis Pipeline
License: MIT License
When running multiple cellbender jobs from the same directory (multiSAP in our case), ckpt.tar.gz was being overwritten by different jobs, therefore causing an error.
cellbender issue page about checkpoint
example log file from us: cellbender-1142095.log
We need to find a way to run this Cellbender in separate subfolders...
(didn't realized it because previously gpu was so heavily occupied lol)
change wrapper to "v2.9.0/bio/multiqc" then it will work :)
shell:
"""
# common error resolved by those two export commands
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
# run mgatk command
mgatk tenx -i {params.bam} -n {wildcards.sample} -o {OUTDIR}/{wildcards.sample}/mgatk/ \
-bt CB -b {input.tsv}
"""
change from -o {OUTDIR}/{wildcards.sample}/mgatk/
to -o {OUTDIR}/{wildcards.sample}/mgatk
(remove the /
)
Add - ruamel.yaml=0.17.21
dependency to the mgatk environment
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.