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| author | AndreaGuarracino | 2021-01-04 18:41:38 +0100 |
|---|---|---|
| committer | AndreaGuarracino | 2021-01-04 18:41:38 +0100 |
| commit | 491b39273b54ca89861febf5c27d28f032ba1c49 (patch) | |
| tree | 79a791a879dac14ca93b3d1c40e2f7c792e60c70 | |
| parent | f9f27a787fef0ad58c1ae465d8ba1ee4634083ae (diff) | |
| download | bh20-seq-resource-491b39273b54ca89861febf5c27d28f032ba1c49.tar.gz bh20-seq-resource-491b39273b54ca89861febf5c27d28f032ba1c49.tar.lz bh20-seq-resource-491b39273b54ca89861febf5c27d28f032ba1c49.zip | |
created placeholder for the YAML+FASTA to TTL workflow
| -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 + |