Kallisto RNAseq Workflow
Version 1

Workflow Type: Common Workflow Language

Workflow Kallisto RNAseq

(pseudoalignment on transcripts)

All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

How to setup and use an UNLOCK workflow:


ID Name Description Type
identifier Identifier Identifier for this dataset used in this workflow
  • string
threads Threads Number of threads to use for computational processes
  • int?
memory Maximum memory in MB Maximum memory usage in megabytes
  • int?
filter_rrna Filter rRNA Optionally remove rRNA sequences from the reads.
  • boolean
forward_reads Forward reads Forward sequence file locally
  • string[]
reverse_reads Reverse reads Reverse sequence file locally
  • string[]
kallisto_index kallisto index file kallisto index file location
  • string
contamination_references Reference filters files Reference fasta file(s) for filtering (optional)
  • string[]?
destination Output Destination Optional Output destination used for cwl-prov reporting.
  • string?


ID Name Description
workflow_quality Quality and filtering workflow Quality assessment of illumina reads with rRNA filtering option
kallisto kallisto Calculates transcript abundances
kallisto_files_to_folder kallisto output Preparation of kallisto output files to a specific output folder


ID Name Description Type
illumina_quality_stats Filtered statistics Statistics on quality and preprocessing of the reads
  • Directory
kallisto_output kallisto output kallisto results folder. Contains transcript abundances, run info and summary.
  • Directory

Version History

Version 1 (earliest) Created 20th May 2022 at 11:10 by Bart Nijsse

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Views: 1103

Created: 20th May 2022 at 11:10

Last updated: 2nd Nov 2022 at 15:26

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