Skip to content

rnaseq-nf

Proof of concept of a RNA-seq pipeline implemented with Nextflow

Inputs

Input/output options

Name Description Type Default Required
--outdir The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. string results no
--reads The input read-pair files string ${projectDir}/data/ggal/ggal_gut_{1,2}.fq no
--transcriptome The input transcriptome file string ${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa no
--multiqc n/a string ${projectDir}/multiqc no

Workflows

Name Description Entry
(entry) n/a yes
RNASEQ n/a no

RNASEQ Inputs

Name Description
read_pairs_ch n/a
transcriptome n/a

RNASEQ Outputs

Name Description
fastqc n/a
quant n/a

Processes

Name Description
QUANT n/a
MULTIQC n/a
INDEX n/a
FASTQC n/a

QUANT Inputs

Name Type Description
val(id), path(fastq_1), path(fastq_2) tuple n/a

QUANT Outputs

Name Type Emit Description
quant_${id path n/a n/a

MULTIQC Inputs

Name Type Description
* path n/a

MULTIQC Outputs

Name Type Emit Description
multiqc_report.html path n/a n/a

INDEX Outputs

Name Type Emit Description
index path n/a n/a

FASTQC Inputs

Name Type Description
val(id), path(fastq_1), path(fastq_2) tuple n/a

FASTQC Outputs

Name Type Emit Description
fastqc_${id path n/a n/a

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.2.0 on 2026-03-03 22:40:53 UTC.