DGE-DESEQ2 (⚠ ACTIVE DEVELOPMENT)

Version: 1.0.0 Tags: DESeq2 / Salmon / DGE / Flamingo / Automated

This is the fully automated pipeline for differential gene expression on Flamingo. No config, no stats, no time wasted.

« A good pipeline has no documentation » Someone at BiGR

This is not a good pipeline: it requires documentation. Please read the notes to have information on design file format.

Pipeline dependencies

This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.

Conda:

  • conda-forge::python ==3.9.2

  • conda-forge::git ==2.30.2

  • conda-forge::jinja2 ==2.11.3

  • conda-forge::pygraphviz ==1.7

  • conda-forge::flask ==1.1.2

  • conda-forge::pandas ==1.2.3

  • conda-forge::zlib ==1.2.11

  • conda-forge::openssl ==1.1.1k

  • conda-forge::networkx ==2.5.1

  • bioconda::snakemake ==6.1.1

  • conda-forge::black ==20.8b1

  • conda-forge::singularity ==3.7.1

  • conda-forge::mamba ==0.9.2

Additionally, the following prerequisites are non-optional:

  • None. Everything is on Flamingo already.

Input files

Please find below the list of required input files:

  • Several paried fastq files.

Output files

Please find below the list of expected output files:

  • Salmon quantification

  • Differential analysis

  • MultiQC report with additional graphs

Notes

THis pipeline is under active development. THe design format is a TSV formatted text file with the following required columns: Sample_id, Upstream_file, Downstream_file.

Any additional column will be used sequentially as a comparison factor. Their names are free.

Installation

While installing the workflow, you may run the following commands (order matters):

Case

Command line

none

 
# No installation needed.

Testing

In order to test the pipeline, you may try the following commands:

Case

Command line

quick-test

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/dge_deseq2/test.sh

verbose-test

 
bash -x /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/dge_deseq2/test.sh

Preparation

In order to prepare a run, you may try the following commands:

Case

Command line

none

 
# No preparation, everything is available.

Execution

In order to execute the pipeline, you may run the following commands:

Case

Command line(s)

hg19

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/dge_deseq2/run.sh hg19

hg38

 
bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/dge_deseq2/run.sh hg38