Kallisto RNAseq Workflow Version 1
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Download RO CrateWorkflow Kallisto RNAseq
(pseudoalignment on transcripts)
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- kallisto
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:
https://m-unlock.gitlab.io/docs/setup/setup.html
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | Identifier | Identifier for this dataset used in this workflow |
|
| threads | Threads | Number of threads to use for computational processes |
|
| memory | Maximum memory in MB | Maximum memory usage in megabytes |
|
| filter_rrna | Filter rRNA | Optionally remove rRNA sequences from the reads. |
|
| forward_reads | Forward reads | Forward sequence file locally |
|
| reverse_reads | Reverse reads | Reverse sequence file locally |
|
| kallisto_index | kallisto index file | kallisto index file location |
|
| contamination_references | Reference filters files | Reference fasta file(s) for filtering (optional) |
|
| destination | Output Destination | Optional Output destination used for cwl-prov reporting. |
|
Steps
| 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 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| illumina_quality_stats | Filtered statistics | Statistics on quality and preprocessing of the reads |
|
| kallisto_output | kallisto output | kallisto results folder. Contains transcript abundances, run info and summary. |
|
Version History
Version 1 (earliest) Created 20th May 2022 at 11:10 by Bart Nijsse
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Created: 20th May 2022 at 11:10
Last updated: 2nd Nov 2022 at 15:26
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