Spliced RNAseq workflow
Version 1

Workflow Type: Common Workflow Language

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)

Click and drag the diagram to pan, double click or use the controls to zoom.


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
  • <strong>enum</strong> of: None, TranscriptomeSAM, GeneCounts


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


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

Version History

Version 1 (earliest) Created 22nd Dec 2020 at 15:53 by Bart Nijsse

Added/updated 1 files

Open master 168dee2
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Views: 1926   Downloads: 172

Created: 22nd Dec 2020 at 15:53

Last updated: 8th Jun 2021 at 13:31

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