diff options
Diffstat (limited to 'workflows')
| -rw-r--r-- | workflows/yamlfa2ttl/yamlfa2ttl.cwl | 31 |
1 files changed, 31 insertions, 0 deletions
diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl new file mode 100644 index 0000000..2580794 --- /dev/null +++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl @@ -0,0 +1,31 @@ +#!/usr/bin/env cwl-runner + +cwlVersion: v1.1 +class: CommandLineTool +doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)" + +inputs: + path_fasta: + type: File + inputBinding: + position: 1 + path_yaml: + type: File + inputBinding: + position: 2 + +steps: + check_format: + in: {path_fasta: path_fasta, path_valid_formats: '../../bh20sequploader/validation/formats', format_to_check: 'text/fasta'} + #out: true/false or nothing and it has to block the execution if the format is wrong + run: check_format.cwl + check_metadata: + # input and output + # run: check_metadata.cwl + check_header: + # id_fasta has to be equal to id_yaml + # run: check_header.cwl + check_sequence: + # The sequence has to be similar to the reference + # run: check_sequence.cwl + |