NonSpliced RNAseq workflow
Version 1

Work-in-progress

Workflow for NonSpliced RNAseq data with multiple aligners.

Steps:

- workflow_quality.cwl:

    - FastQC (control)

    - fastp (trimming)

- bowtie2 (read mapping)

- sam_to_sorted-bam

- featurecounts (transcript read counts)

- kallisto (transcript [pseudo]counts)

SEEK ID: https://workflowhub.eu/workflows/77?version=1

Inputs

ID	Name	Description	Type
threads	number of threads	number of threads to use for computational processes	int?
memory	Max memory	maximum memory usage in megabytes	int?
filter_rrna	Filer rRNA	Filter rRNA from reads if true	boolean
prefix_id	Filename prefix	Prefix of the output filenames.	string
forward_reads	forward reads	forward sequence file locally	File
reverse_reads	reverse reads	reverse sequence file locally	File
bowtie2-indexfolder	bowtie2 index	Folder location of the bowtie2 index files.	Directory
kallisto-indexfolder	kallisto index	Folder location of the kallisto index file.	Directory?
gtf	GTF file	GTF file location	File?

Steps

ID	Name	Description
quality	Quality and filtering workflow	Quality assessment of illumina reads with rRNA filtering option
bowtie2	bowtie2	runs bowtie2 alignment on the genome with the quality filtered reads.
sam_to_sorted-bam	sam to sorted bam	Converts a SAM file to a sorted BAM file
featurecounts	FeatureCounts	Calculates gene counts with bowtie2 mapped data and input GTF file with FeatureCounts.
kallisto	kallisto	Calculates transcript abundances
bowtie2_files_to_folder	bowtie2 output	Preparation of bowtie2 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	FeatureCounts 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_bowtie2	bowtie2 output	bowtie2 mapping results folder. Contains sorted bam file, metrics file and mapping statistics (stdout).	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