Workflow Documentation:

KU GDSC developed workflows:

1. Microbial RNA-seq: microbial_rnaseq

Quick Start for KU Users

An example run script to run the microbial RNAseq pipeline

#!/bin/bash
#SBATCH --job-name=microbial_rnaseq
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=<USERNAME>@ku.edu
#SBATCH --ntasks=1
#SBATCH --cpus-per-task 1
#SBATCH --time=24:00:00
#SBATCH --partition=sjmac
#SBATCH --mem=10G
#SBATCH --output=%x_%A.out

module use --append /panfs/pfs.local/work/sjmac/observer/modules
module load nextflow

NXF_ANSI_SUMMARY=true
NXF_ANSI_LOG=true

nextflow run ku-gdsc/workflows \
    -r main \
    --workflow microbial_rnaseq \
    --fasta /PATH/TO/FASTA \
    --gff /PATH/TO/GFF \
    --sample_folder /PATH/TO/FASTQ/FILES \
    --pubdir /PATH/TO/OUTPUT/RESULTS \
    -w /PATH/TO/WORK/DIRECTORY \
    --strandedness reverse_stranded \
    -resume

Notes:

1. This example runs the microbial RNA-seq workflow. It requires the specification of a reference FASTA, a GFF3, and a folder of FASTQ files (not provided here). See the full workflow documentation for additional detail

2. For all pipelines, running the flag --help (e.g, ~/nextflow <PATH>/<TO>/main.nf --workflow microbial_rnaseq --help) will print help documentation for that pipeline and quit.

---

Last update: January 13, 2024