RNAseq pipeline
- Source code: https://github.com/pilm-bioinformatics/pipelines-nf-rnaseq
- Documentation: https://pilm-bioinformatics.github.io/pipelines-nf-rnaseq/
- Public dataset browser: https://ewels.github.io/sra-explorer/#
Scheme
Pipeline Overview: https://pilm-bioinformatics.github.io/pipelines-nf-rnaseq/output.html
- The pipeline is defined in the
main.nffile - The config files are defined in:
nextflow.configand all the files in theconffolder.
Logging
Important parameters
Some parameters that have an important impact to the computer resources requirements and time execution.
--pseudo_aligner salmon: to run best practices for gene/transcript quantification--singleEnd: in case of not being paired dataset--aligner hisat2: to reduce the resources during alignment (if salmon is on)--skipGenebodyCoverage: long process that gives the same information than Qualimap--skipDupRadar: long process that gives similar information than Qualimap--skipPreseq: long process that gives similar information than Qualimap--skipRseQC: long process that gives similar information than Qualimap
All parameters are defined at nextflow.config
Reports
- output explanation
- execution_timeline.html
- execution_report.html
- results_description.html
- software_versions.csv