Revert "add nextflow schema"

CHANGELOG.md

@@ -1,11 +1,3 @@
-# viash_project_template 0.3.0
-
-* Update to Viash 0.8.2
-
-    * `demo_pipeline` is now built from `src/workflows/demo_pipeline`
-    * State management overhaul
-    * Use of helper functions (dependencies) from [`vsh_utils`](https://viash-hub.com/data-intuitive/vsh_utils)
-
 # viash_project_template 0.2.0
 
 * Update to Viash 0.7.1.
@@ -30,4 +22,4 @@ Components:
 
 Pipelines:
 
-* `workflows/demo_pipeline/main.nf`: A demo pipeline which uses abovementioned components.
+* `workflows/demo_pipeline/main.nf`: A demo pipeline which uses abovementioned components.

_viash.yaml

@@ -1,10 +1,10 @@
-viash_version: 0.8.4
+viash_version: 0.7.1
 
 source: src
 target: target
 
 config_mods: |
-  .functionality.version := '0.2.2'
+  .functionality.version := 'dev'
   .platforms[.type == 'docker'].target_registry := 'ghcr.io'
   .platforms[.type == 'docker'].target_organization := 'viash-io/viash_project_template'
   .platforms[.type == 'docker'].target_image_source := 'https://github.com/viash-io/viash_project_template'

src/template/combine_columns/config.vsh.yaml → src/demo/combine_columns/config.vsh.yaml

@@ -1,6 +1,6 @@
 functionality:
   name: combine_columns
-  namespace: template
+  namespace: demo
   arguments:
     - name: "--input"
       alternatives: [ "-i" ]
@@ -12,10 +12,13 @@ functionality:
       type: file
       required: true
       direction: output
+    - type: string
+      name: --id
+      default: "combine_columns"
   resources:
     - type: r_script
       path: script.R
 platforms:
   - type: docker
     image: eddelbuettel/r2u:22.04
-  - type: nextflow
+  - type: nextflow

src/template/remove_comments/config.vsh.yaml → src/demo/remove_comments/config.vsh.yaml

@@ -1,6 +1,6 @@
 functionality:
   name: remove_comments
-  namespace: template
+  namespace: demo
   arguments:
     - name: "--input"
       alternatives: [ "-i" ]
@@ -13,12 +13,15 @@ functionality:
       required: true
       direction: output
       example: "file.tsv"
+    - type: string
+      name: --id
+      default: "remove_comments"
   resources:
-    - type: bash_script
-      path: script.sh
+  - type: bash_script
+    path: script.sh
   test_resources:
-    - type: bash_script
-      path: test.sh
+  - type: bash_script
+    path: test.sh
 platforms:
   - type: docker
     image: ubuntu:20.04

src/template/take_column/config.vsh.yaml → src/demo/take_column/config.vsh.yaml

@@ -1,6 +1,6 @@
 functionality:
   name: take_column
-  namespace: template
+  namespace: demo
   arguments:
     - name: "--input"
       alternatives: [ "-i" ]
@@ -15,6 +15,9 @@ functionality:
       type: integer
       required: false
       default: 2
+    - type: string
+      name: --id
+      default: "take_column"
   resources:
   - type: python_script
     path: script.py
@@ -23,9 +26,5 @@ platforms:
     image: python:3.10-slim
     setup:
       - type: python
-        packages: 
-          - pandas
-      - type: apt
-        packages: 
-          - procps
+        packages: pandas
   - type: nextflow