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MIGNON is a bioinformatic workflow for the mechanistic integrative analysis of rna-seq data. It is written using the Workflow Description Language (WDL) and can be executed using Cromwell. It implements a novel way of analyzing RNA-Seq data, extracting the transcriptomic and genomic information obtainable from RNA-Seq reads. By using a in-silico knockdown strategy, it estimates the cellular signaling circuits activities through the application of the hipathia model, using gene expression as a proxy of protein signaling activity.
In order to execute the workflow, the user needs to be able of launching the Cromwell engine, regardless of where it is deployed. We recommend reading the Five Minutes Intro created by the Broad Institute team, which explain the basic operations that can be performed using their software. Additionally, as the tools employed by the workflow are used as docker containers, the system where the pipeline is deployed should dispose of an engine to run such containers. Particularly, we have tested the workflow both locally with Docker and in a High Performance Computing (HPC) environment, executing the containers as Singularity images. Theoretically, it is also deployable within the Terra platform, which makes use of cloud computing services to execute the WDL workflows.
In order to execute MIGNON with Cromwell, we have prepared two configuration files to run the workflow both locally and in a Slurm + Singularity HPC environment. They can be found at the config directory. After preparing the [input and the Cromwell jar, users can clone the repository:
$ git clone https://github.com/babelomics/MIGNON.git
$ cd MIGNON
And execute MIGNON locally with docker:
$ java -Dconfig.file=configs/LocalWithDocker.conf -jar /path/to/cromwell.jar run wdl/MIGNON.wdl /path/to/input.json
Or in HPC environments with Slurm and Singularity:
$ java -Dconfig.file=configs/SlurmAndSingularity.conf -jar /path/to/cromwell.jar run wdl/MIGNON.wdl /path/to/input.json
The following containers are used during the execution of the workflow:
| Tool | Version | Docker container |
|---|---|---|
| fastp | v0.20.0 | quay.io/biocontainers/fastp:0.20.0 |
| fastqc | v0.11.5 | biocontainers/fastqc:v0.11.5_cv4 |
| samtools | v1.9 | quay.io/biocontainers/samtools:1.9 |
| HISAT2 | v2.1.0 | quay.io/biocontainers/hisat2:2.1.0 |
| STAR | v.2.7.2b | quay.io/biocontainers/star:2.7.2b |
| salmon | v.0.13.0 | quay.io/biocontainers/salmon:0.13.0 |
| GATK | v4.1.3.0 | broadinstitute/gatk:4.1.3.0 |
| picard | v2.20.7 | broadinstitute/picard:2.20.7 |
| VeP | v99 | ensemblorg/ensembl-vep:release_99.1 |
| txImport | v1.10.0 | quay.io/biocontainers/bioconductor-tximport:1.10.0 |
| edgeR | v3.28.0 | quay.io/biocontainers/bioconductor-edger:3.28.0 |
| hipathia | v2.2.0 | quay.io/biocontainers/bioconductor-hipathia:2.2.0 |