Manu fix star issue - Githubissues

lifebit-ai / nf-rnaseq-salmon

MIT License

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Manu fix star issue #7

Open manu-lifebit opened 2 years ago

manu-lifebit commented 2 years ago

Overview

The main purpose of this PR is to address this issue https://github.com/lifebit-ai/nf-rnaseq-salmon/issues/4

Purpose

To achieve that we modified the memory usage params in each process.

Changes

Refactor main.nf
Refactor base.config
Refactor nextflow.config
Create new profile config files.

Testing

In order to run the script locally:

Clone the repository:

git clone https://github.com/lifebit-ai/nf-rnaseq-salmon.git
cd nf-rnaseq-salmon
git checkout manu-fix-star-issue

Execute the nextflow pipeline
```
NXF_VER=20.04.1 nextflow run main.nf --config conf/minimal_star_yeast_test.config
```
Results: The pipeline will generate the read count files in the results folder

CloudOS test runs:

https://lifebit.atlassian.net/browse/DEL-5411

NOTES: The human runs showed minimal errors described in https://github.com/lifebit-ai/nf-rnaseq-salmon/issues/9 https://github.com/lifebit-ai/nf-rnaseq-salmon/issues/8 which should be addressed in the next PR.

All the datasets used are described in https://docs.google.com/document/d/1R0ypiaf7xfidrEWOZ1hnkHDlWLKQ9CtEhUWGrqWS9LU/edit?usp=sharing

All the runs with star or hisat should be performed in a machine with >=100GB RAM and 10-16 cpus.