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kids-first / kf-rnaseq-workflow

:microscope: RNA-Seq workflow for Kids-First DRC
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ID clashes for arriba and kallisto #23

Open illusional opened 3 years ago

illusional commented 3 years ago

There are a couple of tools where the IDs clash, for example:

arriba_draw_fusion.cwl and arriba_fusion.cwl

https://github.com/kids-first/kf-rnaseq-workflow/blob/3e68956d910f8fb792414805386b6fca2f11b92c/tools/arriba_draw_fusion.cwl#L3

https://github.com/kids-first/kf-rnaseq-workflow/blob/3e68956d910f8fb792414805386b6fca2f11b92c/tools/arriba_fusion.cwl#L3

kallisto_calc_expression.cwl and kallisto_calc_expression_with_fusion.cwl

https://github.com/kids-first/kf-rnaseq-workflow/blob/3e68956d910f8fb792414805386b6fca2f11b92c/tools/kallisto_calc_expression.cwl#L3

https://github.com/kids-first/kf-rnaseq-workflow/blob/3e68956d910f8fb792414805386b6fca2f11b92c/tools/kallisto_calc_expression_with_fusion.cwl#L3

Suggested fix:

diff --git a/tools/arriba_draw_fusion.cwl b/tools/arriba_draw_fusion.cwl
index faf1dcf..39d6da1 100644
--- a/tools/arriba_draw_fusion.cwl
+++ b/tools/arriba_draw_fusion.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.0
 class: CommandLineTool
-id: arriba_fusion
+id: arriba_draw_fusion
 requirements:
   - class: ShellCommandRequirement
   - class: DockerRequirement
diff --git a/tools/kallisto_calc_expression_with_fusion.cwl b/tools/kallisto_calc_expression_with_fusion.cwl
index b6860ed..a7ccf72 100644
--- a/tools/kallisto_calc_expression_with_fusion.cwl
+++ b/tools/kallisto_calc_expression_with_fusion.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.0
 class: CommandLineTool
-id: kallisto
+id: kallisto_with_fusion
 requirements:
   - class: ShellCommandRequirement
   - class: DockerRequirement