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authorAndreaGuarracino2021-01-08 23:44:47 +0100
committerAndreaGuarracino2021-01-08 23:44:47 +0100
commit53a47a18a45270c3f037fabe9cc973c66bfe50bf (patch)
tree1fb71fae0d629127a5da6f9ad879fff259016b14 /workflows/yamlfa2ttl/yamlfa2ttl.cwl
parent2ddf72a4028475eb65dfeab153f3565e698d5338 (diff)
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sample_id in the FASTA has to match the sample_id in the YAMLyamlfa2ttl
Diffstat (limited to 'workflows/yamlfa2ttl/yamlfa2ttl.cwl')
-rw-r--r--workflows/yamlfa2ttl/yamlfa2ttl.cwl20
1 files changed, 7 insertions, 13 deletions
diff --git a/workflows/yamlfa2ttl/yamlfa2ttl.cwl b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
index 2913e99..563f00f 100644
--- a/workflows/yamlfa2ttl/yamlfa2ttl.cwl
+++ b/workflows/yamlfa2ttl/yamlfa2ttl.cwl
@@ -1,10 +1,3 @@
-~/.config/guix/current/bin/guix environment -C guix --ad-hoc cwltool python python-biopython python-requests python-dateutil python-magic ruby
-cwltool --preserve-environment PYTHONPATH yamlfa2ttl.cwl --path_fasta ~/bh20-seq-resource/example/sequence.fasta
-
-cwltool --no-container --preserve-environment GUIX_ENVIRONMENT --preserve-environment PYTHONPATH yamlfa2ttl.cwl --path_fasta ~/bh20-seq-resource/example/sequence.fasta
-
-
-
#!/usr/bin/env cwl-runner
cwlVersion: v1.1
@@ -12,7 +5,7 @@ class: Workflow
doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)"
inputs:
- path_fasta:
+ path-fasta:
type: string
doc: input FASTA to validate
@@ -20,14 +13,14 @@ inputs:
type: string
default: text/fasta
- path_yaml:
+ path-yaml:
type: string
doc: input YAML to validate and convert in TTL
steps:
check_format:
in:
- path_fasta: path_fasta
+ path_fasta: path-fasta
format_to_check: format_to_check
doc: the input has to be a valid FASTA format file
out: []
@@ -35,15 +28,16 @@ steps:
check_sequence:
in:
- path_fasta: path_fasta
+ path_fasta: path-fasta
doc: the input sequence has to be enough similar to the reference
out: []
run: check_sequence.cwl
check_metadata:
in:
- path_yaml: path_yaml
- doc: the input metadata information to put in the knowledge graph
+ path_yaml: path-yaml
+ path_fasta: path-fasta
+ doc: check the input metadata information to put in the knowledge graph
out: []
run: check_metadata.cwl