From 42469c0a384e62a90e6828b2e429ccac3c97c414 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" <1330696+mr-c@users.noreply.github.com> Date: Thu, 24 Mar 2022 09:06:40 +0100 Subject: [PATCH] use CWL version v1.2 (final not dev) --- .../covid19/genomics/Galaxy-Workflow-COVID-19__Assembly.cwl | 2 +- examples/covid19/genomics/Galaxy-Workflow-COVID-19__MCRA.cwl | 2 +- .../covid19/genomics/Galaxy-Workflow-COVID-19__RecSel.cwl | 2 +- .../covid19/genomics/Galaxy-Workflow-COVID-19__S-gene_AA.cwl | 2 +- .../genomics/Galaxy-Workflow-COVID-19__SE_Variation.cwl | 2 +- ...y-Workflow-COVID-19__read_pre-processing_from_SRA_data.cwl | 2 +- examples/simple_workflow_cwl-interface.cwl | 2 +- examples/simple_workflow_cwl_automatic.cwl | 2 +- examples/simple_workflow_galaxy.cwl | 2 +- galaxy2cwl/get_cwl_interface.py | 4 ++-- 10 files changed, 11 insertions(+), 11 deletions(-) diff --git a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__Assembly.cwl b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__Assembly.cwl index 67a8f4d..df63d03 100644 --- a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__Assembly.cwl +++ b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__Assembly.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.2.0-dev2 +cwlVersion: v1.2 doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: Assembly' inputs: diff --git a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__MCRA.cwl b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__MCRA.cwl index 124fabd..9d930ca 100644 --- a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__MCRA.cwl +++ b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__MCRA.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.2.0-dev2 +cwlVersion: v1.2 doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: MCRA' inputs: diff --git a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__RecSel.cwl b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__RecSel.cwl index 400f641..a0024f5 100644 --- a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__RecSel.cwl +++ b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__RecSel.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.2.0-dev2 +cwlVersion: v1.2 doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: RecSel' inputs: diff --git a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__S-gene_AA.cwl b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__S-gene_AA.cwl index c8978fa..9c9946c 100644 --- a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__S-gene_AA.cwl +++ b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__S-gene_AA.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.2.0-dev2 +cwlVersion: v1.2 doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: S-gene AA' inputs: diff --git a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__SE_Variation.cwl b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__SE_Variation.cwl index 2a6a944..049e1e2 100644 --- a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__SE_Variation.cwl +++ b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__SE_Variation.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.2.0-dev2 +cwlVersion: v1.2 doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: SE Variation' inputs: diff --git a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__read_pre-processing_from_SRA_data.cwl b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__read_pre-processing_from_SRA_data.cwl index e246789..6d7058b 100644 --- a/examples/covid19/genomics/Galaxy-Workflow-COVID-19__read_pre-processing_from_SRA_data.cwl +++ b/examples/covid19/genomics/Galaxy-Workflow-COVID-19__read_pre-processing_from_SRA_data.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.2.0-dev2 +cwlVersion: v1.2 doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: COVID-19: read pre-processing from SRA data' inputs: diff --git a/examples/simple_workflow_cwl-interface.cwl b/examples/simple_workflow_cwl-interface.cwl index 4089de3..ae93a68 100644 --- a/examples/simple_workflow_cwl-interface.cwl +++ b/examples/simple_workflow_cwl-interface.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: Workflow label: Abstract CWL workflow automatically generated from a Galaxy workflow v2 file inputs: diff --git a/examples/simple_workflow_cwl_automatic.cwl b/examples/simple_workflow_cwl_automatic.cwl index d41c4f2..f28b9e8 100644 --- a/examples/simple_workflow_cwl_automatic.cwl +++ b/examples/simple_workflow_cwl_automatic.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.0 +cwlVersion: v1.2 inputs: 0/output: format: Input files have no info about format diff --git a/examples/simple_workflow_galaxy.cwl b/examples/simple_workflow_galaxy.cwl index 02e2ecb..06ee658 100644 --- a/examples/simple_workflow_galaxy.cwl +++ b/examples/simple_workflow_galaxy.cwl @@ -1,5 +1,5 @@ class: Workflow -cwlVersion: v1.2.0-dev2 +cwlVersion: v1.2 doc: 'Abstract CWL Automatically generated from the Galaxy workflow file: Simple workflow' inputs: reads_1: diff --git a/galaxy2cwl/get_cwl_interface.py b/galaxy2cwl/get_cwl_interface.py index 1e351b8..6e51708 100755 --- a/galaxy2cwl/get_cwl_interface.py +++ b/galaxy2cwl/get_cwl_interface.py @@ -120,7 +120,7 @@ def process_format1_json(wf_dict): step_cwl_entry['run'] = step_run_dict step_cwl_entry['out'] = step_wf_out cwl_out['steps']=steps - cwl_out['cwlVersion']='v1.2.0-dev2' + cwl_out['cwlVersion']='v1.2' cwl_out['class']='Workflow' cwl_out['doc']=cwl_doc cwl_out['inputs']=wf_inputs @@ -268,7 +268,7 @@ def process_format2_yaml(wf_dict): wf_outputs[output]=output_details cwl_out={} cwl_out['steps']=steps - cwl_out['cwlVersion']='v1.2.0-dev1' + cwl_out['cwlVersion']='v1.2' cwl_out['class']='Workflow' cwl_out['doc']=cwl_doc cwl_out['inputs']=wf_inputs