Pipeline Inputs

This page documents all input parameters for the pipeline.

Input/output options

--outdir

Type: string | Optional | Format: directory-path

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Default: results

--reads

Type: string | Optional

The input read-pair files

Default: ${projectDir}/data/ggal/ggal_gut_{1,2}.fq

--transcriptome

Type: string | Optional

The input transcriptome file

Default: ${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa

--multiqc

Type: string | Optional

Default: ${projectDir}/multiqc

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.1.0 on 2026-01-23 17:21:40 UTC.