NonSpliced RNAseq workflow
Version 1

Workflow Type: Common Workflow Language

Workflow for NonSpliced RNAseq data with multiple aligners.

- workflow_quality.cwl: - FastQC (control) - fastp (trimming) - bowtie2 (read mapping) - sam_to_sorted-bam - featurecounts (transcript read counts) - kallisto (transcript [pseudo]counts)


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?


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


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

Version History

Version 1 (earliest) Created 24th Nov 2020 at 11:05 by Bart Nijsse

Added/updated 1 files

Open master 533f564
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Views: 1776   Downloads: 64

Created: 24th Nov 2020 at 11:05

Last updated: 8th Jun 2021 at 08:32

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