From 7b009a027cf8b951b24f09ad857af89551d460e3 Mon Sep 17 00:00:00 2001
From: Adrian Zimmer <z.adrian1995@gmail.com>
Date: Sat, 13 Aug 2022 16:59:07 +0200
Subject: [PATCH] Refactor
---
runs/kallisto_collect/kallisto_collect.yml | 2 +-
runs/kallisto_index/run.cwl | 2 +-
runs/merged_isa_metadata/merge_isa_metadata.yml | 2 +-
workflows/kallisto_collect/workflow.cwl | 7 ++-----
workflows/kallisto_index/workflow.cwl | 7 ++-----
workflows/kallisto_quant/workflow.cwl | 1 -
workflows/kallisto_sleuth/workflow.cwl | 5 ++---
workflows/merge_isa_metadata/workflow.cwl | 5 ++---
workflows/shiny_prep/workflow.cwl | 7 ++-----
9 files changed, 13 insertions(+), 25 deletions(-)
diff --git a/runs/kallisto_collect/kallisto_collect.yml b/runs/kallisto_collect/kallisto_collect.yml
index fa4ee11..78c3462 100644
--- a/runs/kallisto_collect/kallisto_collect.yml
+++ b/runs/kallisto_collect/kallisto_collect.yml
@@ -7,4 +7,4 @@ in_metadata_file:
path: ../merged_isa_metadata/merged_isa.tsv
in_metadata_sample: "Sample.Name.2"
in_metadata_factor: "Factor..Photosynthesis.mode."
-out_folder: out
\ No newline at end of file
+out_folder: out
diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl
index efca83d..848b96d 100644
--- a/runs/kallisto_index/run.cwl
+++ b/runs/kallisto_index/run.cwl
@@ -18,4 +18,4 @@ steps:
in:
in_genome_ref: in_genome_ref
out_folder: out_folder
- out: [outdir]
\ No newline at end of file
+ out: [outdir]
diff --git a/runs/merged_isa_metadata/merge_isa_metadata.yml b/runs/merged_isa_metadata/merge_isa_metadata.yml
index 4e4d2a1..675e868 100644
--- a/runs/merged_isa_metadata/merge_isa_metadata.yml
+++ b/runs/merged_isa_metadata/merge_isa_metadata.yml
@@ -5,4 +5,4 @@ in_isa_study:
in_isa_assay:
class: File
path: ../../assays/Talinum_RNASeq_minimal/isa.assay.xlsx
-out_folder: out
\ No newline at end of file
+out_folder: out
diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/kallisto_collect/workflow.cwl
index 73f215d..a109fb0 100644
--- a/workflows/kallisto_collect/workflow.cwl
+++ b/workflows/kallisto_collect/workflow.cwl
@@ -1,5 +1,4 @@
#!/usr/bin/env cwl-runner
-
cwlVersion: v1.2.0-dev1
class: CommandLineTool
hints:
@@ -10,6 +9,8 @@ requirements:
listing:
- class: File
location: kallisto_collect.R
+baseCommand:
+- Rscript
arguments:
- position: 0
valueFrom: kallisto_collect.R
@@ -34,7 +35,6 @@ inputs:
type: string
inputBinding:
position: 5
-
outputs:
- id: outdir
type:
@@ -42,6 +42,3 @@ outputs:
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file
diff --git a/workflows/kallisto_index/workflow.cwl b/workflows/kallisto_index/workflow.cwl
index a91a17c..f102e5c 100644
--- a/workflows/kallisto_index/workflow.cwl
+++ b/workflows/kallisto_index/workflow.cwl
@@ -1,5 +1,4 @@
#!/usr/bin/env cwl-runner
-
cwlVersion: v1.2.0-dev1
class: CommandLineTool
hints:
@@ -10,6 +9,8 @@ requirements:
listing:
- class: File
location: kallisto_index.sh
+baseCommand:
+- bash
arguments:
- position: 0
valueFrom: ./kallisto_index.sh
@@ -22,7 +23,6 @@ inputs:
type: string
inputBinding:
position: 2
-
outputs:
- id: outdir
type:
@@ -30,6 +30,3 @@ outputs:
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- bash
\ No newline at end of file
diff --git a/workflows/kallisto_quant/workflow.cwl b/workflows/kallisto_quant/workflow.cwl
index 5b45601..90aa9da 100644
--- a/workflows/kallisto_quant/workflow.cwl
+++ b/workflows/kallisto_quant/workflow.cwl
@@ -1,5 +1,4 @@
#!/usr/bin/env cwl-runner
-
cwlVersion: v1.2.0-dev1
class: CommandLineTool
hints:
diff --git a/workflows/kallisto_sleuth/workflow.cwl b/workflows/kallisto_sleuth/workflow.cwl
index 009ea53..ec2800b 100644
--- a/workflows/kallisto_sleuth/workflow.cwl
+++ b/workflows/kallisto_sleuth/workflow.cwl
@@ -10,6 +10,8 @@ requirements:
listing:
- class: File
location: kallisto_sleuth.R
+baseCommand:
+- Rscript
arguments:
- position: 0
valueFrom: kallisto_sleuth.R
@@ -29,6 +31,3 @@ outputs:
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file
diff --git a/workflows/merge_isa_metadata/workflow.cwl b/workflows/merge_isa_metadata/workflow.cwl
index 436cc7d..c6066ed 100644
--- a/workflows/merge_isa_metadata/workflow.cwl
+++ b/workflows/merge_isa_metadata/workflow.cwl
@@ -10,6 +10,8 @@ requirements:
listing:
- class: File
location: merge_isa_metadata.R
+baseCommand:
+- Rscript
arguments:
- position: 0
valueFrom: merge_isa_metadata.R
@@ -34,6 +36,3 @@ outputs:
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
diff --git a/workflows/shiny_prep/workflow.cwl b/workflows/shiny_prep/workflow.cwl
index db3ff8b..4caf713 100644
--- a/workflows/shiny_prep/workflow.cwl
+++ b/workflows/shiny_prep/workflow.cwl
@@ -1,5 +1,4 @@
#!/usr/bin/env cwl-runner
-
cwlVersion: v1.2.0-dev1
class: CommandLineTool
hints:
@@ -10,6 +9,8 @@ requirements:
listing:
- class: File
location: shiny_prep.R
+baseCommand:
+- Rscript
arguments:
- position: 0
valueFrom: shiny_prep.R
@@ -22,7 +23,6 @@ inputs:
type: File
inputBinding:
position: 2
-
outputs:
- id: outdir
type:
@@ -30,6 +30,3 @@ outputs:
items: Directory
outputBinding:
glob: $(runtime.outdir)/$(inputs.out_folder)
-
-baseCommand:
-- Rscript
\ No newline at end of file
--
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