Nextflow workshop completed during residential training programme in December 2021 as part of the PhD Programme in Genomics Data Science.
Scripts written for Nextflow v21.04.1 https://github.com/nextflow-io/nextflow/releases/download/v21.04.1/nextflow
main.nf implements bulk RNA-seq analysis using Kallisto, including:
- fastQC and multiQC.
- The option to generate a transcriptome and/or an indexed transcriptome or pass one to the script (using
params.transcriptomeorparams.index). This option is provided through the use of ternary operators and conditionals. - RNA quantification using
kallisto quant.
This also implements continuous implementation to test main.nf using a minimal dataset.
To run:
nextflow pull kevinpryan/rtp_workshop
nextflow run -r dev kevinpryan/rtp_workshop