From 5e97d677251e00cfa8663803b9c39916286e5ac3 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 19 Dec 2022 12:57:40 +0100
Subject: [PATCH] CWL input objects don't need to define $namespaces or
 $schemas if the workflow already defines those.

---
 inputs/extract_regions.yml           | 6 ------
 inputs/metaeuk_inputs.yml            | 5 -----
 inputs/metaeuk_to_regions_inputs.yml | 5 -----
 inputs/queue_workflow_inputs.yml     | 5 -----
 inputs/spaln_input.yml               | 5 -----
 inputs/workflow1_inputs.yml          | 5 -----
 6 files changed, 31 deletions(-)

diff --git a/inputs/extract_regions.yml b/inputs/extract_regions.yml
index caa6d37..8d118c9 100644
--- a/inputs/extract_regions.yml
+++ b/inputs/extract_regions.yml
@@ -6,9 +6,3 @@ region_file:
   class: File
   format: iana:text/plain
   path: /home/pvh/Documents/code/Masters/protein_evidence_mapping/data/proteins1.txt
-
-$namespaces:
-  edam: http://edamontology.org/
-  iana: https://www.iana.org/assignments/media-types/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl
\ No newline at end of file
diff --git a/inputs/metaeuk_inputs.yml b/inputs/metaeuk_inputs.yml
index dc3be49..573dbd5 100644
--- a/inputs/metaeuk_inputs.yml
+++ b/inputs/metaeuk_inputs.yml
@@ -9,8 +9,3 @@ query:
 output_name: test.fasta
 max_intron: 1000000
 min_coverage: 0.01
-
-$namespaces:
-  edam: http://edamontology.org/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl
\ No newline at end of file
diff --git a/inputs/metaeuk_to_regions_inputs.yml b/inputs/metaeuk_to_regions_inputs.yml
index 9f4ede8..eec3ef6 100644
--- a/inputs/metaeuk_to_regions_inputs.yml
+++ b/inputs/metaeuk_to_regions_inputs.yml
@@ -2,8 +2,3 @@ metaeuk_fasta:
   class: File
   path: /home/pvh/Documents/code/Masters/protein_evidence_mapping/data/metaeuk_out.fasta
   format: edam:format_1929
-
-$namespaces:
-  edam: http://edamontology.org/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl
\ No newline at end of file
diff --git a/inputs/queue_workflow_inputs.yml b/inputs/queue_workflow_inputs.yml
index 7028033..415b9ba 100644
--- a/inputs/queue_workflow_inputs.yml
+++ b/inputs/queue_workflow_inputs.yml
@@ -7,8 +7,3 @@ proteins_fasta:
   format: edam:format_1929
   path: /usr/people/pvh/seabass/RefSeq_proteins__Cynoglossus_semilaevis.fasta
 species_table: cynosemi
-  
-$namespaces:
-  edam: http://edamontology.org/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl
\ No newline at end of file
diff --git a/inputs/spaln_input.yml b/inputs/spaln_input.yml
index aef5c16..fb1cd26 100644
--- a/inputs/spaln_input.yml
+++ b/inputs/spaln_input.yml
@@ -8,8 +8,3 @@ query_fasta:
   path: /home/pvh/Documents/code/Masters/protein_evidence_mapping/data/protein1.fasta
 species: cynosemi
 output_format: 0
-
-$namespaces:
-  edam: http://edamontology.org/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl
\ No newline at end of file
diff --git a/inputs/workflow1_inputs.yml b/inputs/workflow1_inputs.yml
index a977dca..1abeba2 100644
--- a/inputs/workflow1_inputs.yml
+++ b/inputs/workflow1_inputs.yml
@@ -11,8 +11,3 @@ metaeuk_output:
   format: edam:format_1929
   path: /home/pvh/Documents/code/Masters/protein_evidence_mapping/data/metaeuk_out.fasta
 species_table: cynosemi
-
-$namespaces:
-  edam: http://edamontology.org/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl
\ No newline at end of file