Spliced RNAseq workflow
Version 1

Work-in-progress

Workflow for Spliced RNAseq data

Steps:

- workflow_quality.cwl:

    - FastQC (Read Quality Control)

    - fastp (Read Trimming)

- STAR (Read mapping)

- featurecounts (transcript read counts)

- kallisto (transcript [pseudo]counts)

SEEK ID: https://workflowhub.eu/workflows/95?version=1

Inputs

ID	Name	Description	Type
threads	number of threads	number of threads to use for computational processes	int?
memory	maximum memory usage in megabytes	maximum memory usage in megabytes	int?
filter_rrna	n/a	n/a	boolean
prefix_id	n/a	prefix of the filename outputs	string
forward_reads	forward reads	forward sequence file locally	File
reverse_reads	reverse reads	reverse sequence file locally	File
STAR-indexfolder	folder where the STAR indices are	n/a	Directory
kallisto-indexfolder	folder where the kallisto indices are	n/a	Directory?
gtf	n/a	gtf file	File
quantMode	n/a	Run with get gene quantification	{"type"=>"enum", "symbols"=>["None", "TranscriptomeSAM", "GeneCounts"]} (Optional)

Steps

ID	Name	Description
quality	Quality and filtering workflow	Quality assessment of illumina reads with rRNA filtering option
STAR	STAR	runs STAR alignment on the genome with the quality filtered reads.
featurecounts	FeatureCounts	Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts.
kallisto	kallisto	Calculates transcript abundances
STAR_files_to_folder	STAR output	Preparation of STAR output files to a specific output folder
featurecounts_files_to_folder	FeatureCounts output	Preparation of FeatureCounts output files to a specific output folder
kallisto_files_to_folder	kallisto output	Preparation of kallisto output files to a specific output folder

Outputs

ID	Name	Description	Type
files_to_folder_fastqc	FASTQC	Quality reporting by FASTQC	Directory
files_to_folder_filtered	Filtered reads folder	Output folder with filtered reads.	Directory
files_to_folder_STAR	STAR output folder	STAR results folder. Contains logs, bam file, readcounts per gene and splice_junctions.	Directory
files_to_folder_featurecounts	FeatureCounts output	FeatureCounts results folder. Contains readcounts, summary and mapping statistics (stdout).	Directory
files_to_folder_kallisto	kallisto output	kallisto results folder. Contains transcript abundances, run info and summary.	Directory