Remove input arg from zuani nsclc scripts

Author: LouisK92

src/datasets/loaders/zuani_human_nsclc_sc/config.vsh.yaml

@@ -2,13 +2,13 @@ name: zuani_human_nsclc_sc
 namespace: datasets/loaders
 
 argument_groups:
-  - name: Inputs
-    arguments:
-      - type: file
-        name: --input
-        description: Path to the dataset
-        required: true
-        example: "ftp://anonymous@ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/526/E-MTAB-13526/Files/10X_Lung_Tumour_Annotated_v2.h5ad"
+  #- name: Inputs
+  #  arguments:
+  #    - type: file
+  #      name: --input
+  #      description: Path to the dataset
+  #      required: true
+  #      example: "ftp://anonymous@ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/526/E-MTAB-13526/Files/10X_Lung_Tumour_Annotated_v2.h5ad"
   - name: Caching settings
     arguments:
       - type: boolean
@@ -66,7 +66,7 @@ resources:
 
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
     __merge__: 
       - /src/base/setup_txsim_partial.yaml
   - type: native

src/datasets/workflows/process_zuani_human_nsclc_sc/config.vsh.yaml

@@ -2,13 +2,13 @@ name: process_zuani_human_nsclc_sc
 namespace: datasets/workflows
 
 argument_groups:
-  - name: Inputs
-    arguments:
-      - type: file
-        name: --input
-        description: Path to the dataset
-        required: true
-        example: "ftp://anonymous@ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/526/E-MTAB-13526/Files/10X_Lung_Tumour_Annotated_v2.h5ad"
+  #- name: Inputs
+  #  arguments:
+  #    - type: file
+  #      name: --input
+  #      description: Path to the dataset
+  #      required: true
+  #      example: "ftp://anonymous@ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/526/E-MTAB-13526/Files/10X_Lung_Tumour_Annotated_v2.h5ad"
   - name: Caching settings
     arguments:
       - type: boolean

src/datasets/workflows/process_zuani_human_nsclc_sc/main.nf

@@ -25,7 +25,6 @@ workflow run_wf {
 
     | zuani_human_nsclc_sc.run(
       fromState: [
-        "input",
         "dataset_id",
         "dataset_name",
         "dataset_url",

src/datasets/workflows/process_zuani_human_nsclc_sc/test.sh

@@ -19,7 +19,6 @@ cat > /tmp/params.yaml << HERE
 param_list:
   - id: zuani_human_nsclc_sc/2024Zuani_human_nsclc_sc
         
-input: "ftp://anonymous@ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/526/E-MTAB-13526/Files/10X_Lung_Tumour_Annotated_v2.h5ad"
 keep_files: false 
 
 output_dataset: "\$id/dataset.h5ad"