Workflow: genome-kallisto-index.cwl
Fetched 2026-08-20 17:53:10 GMT
Verified with cwltool version 3.1.20230201224320
Generates a FASTA file with the DNA sequences for all transcripts in a GFF file and builds kallisto index
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| kmer_size | Integer (Optional) |
k-mer (odd) length (default: 31, max value: 31) |
|
| make_unique | Boolean (Optional) |
Replace repeated target names with unique names |
|
| genome_fasta_file | File |
Genome file in FASTA format, uncompressed |
|
| annotation_gtf_file | File |
GTF annotation file |
|
| index_output_filename | String (Optional) |
Filename for the kallisto index to be constructed |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| generate_transcriptome |
gffread.cwl
(CommandLineTool)
|
Generates a FASTA file with the DNA sequences for all transcripts in a GFF file |
|
| generate_kallisto_index |
kallisto-index.cwl
(CommandLineTool)
|
kallisto index builds an index from a FASTA formatted file of target sequences |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| kallisto_index | File | ||
| kallisto_stderr_log | File | ||
| kallisto_stdout_log | File | ||
| transcriptome_fasta_file | File |
Permalink:
https://w3id.org/cwl/view/git/b8e28a017f7b1a2900ec0fd3b3549f123f0c91b4/tools/genome-kallisto-index.cwl
