Merge pull request #75 from mahesh-panchal/annotation_workflow_refactor

Annotation workflow refactor

Author: mahesh-panchal

.gitattributes

@@ -0,0 +1,3 @@
+*.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated

.github/workflows/continuous_integration.yml

@@ -1,20 +1,15 @@
-# This is a basic workflow to help you get started with Actions
-
 name: Continuous Integration
 
 # Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
+# events but only for the master branch, or add_actions branch
 on:
   push:
     branches: [ master, add_actions ]
   pull_request:
     branches: [ master, add_actions ]
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a job called "test"
-  test:
-    # The type of runner that the job will run on
+  test_workflow:
     runs-on: ubuntu-latest
 
     env:
@@ -23,15 +18,14 @@ jobs:
 
     strategy:
       matrix:
-        nxf_ver: ['20.01.0', '']
+        nxf_ver: ['21.10.6', '']
         profile:
-          # - conda
           - docker
         workflow:
-          - ${GITHUB_WORKSPACE}/AbinitioTraining
-          - ${GITHUB_WORKSPACE}/AnnotationPreprocessing
-          # - ${GITHUB_WORKSPACE}/FunctionalAnnotation
-          - ${GITHUB_WORKSPACE}/TranscriptAssembly
+          - 'abinitio_training'
+          - 'annotation_preprocessing'
+          - 'functional_annotation'
+          - 'transcript_assembly'
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -53,4 +47,4 @@ jobs:
     #  run: alias interproscan.sh='docker run biocontainers/interproscan:v5.30-69.0_cv3 /opt/interproscan/interproscan.sh'
 
     - name: Test ${{ matrix.workflow }} with profile ${{ matrix.profile }}
-      run: nextflow run -profile test,${{ matrix.profile }} ${{ matrix.workflow }}
+      run: nextflow run -profile test,${{ matrix.profile }} main.nf --subworkflow ${{ matrix.workflow }}

.gitignore

@@ -1,4 +1,5 @@
 .nextflow*
-pipeline_report/
 results/
-work/
+work/
+
+.DS_Store

.gitpod.yml

@@ -3,12 +3,9 @@ image: nfcore/gitpod:latest
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore                 # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
     - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
-    - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
     - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files
-    - Gruntfuggly.todo-tree                  # Display TODO and FIXME in a tree view in the activity bar
     - mechatroner.rainbow-csv                # Highlight columns in csv files in different colors
-    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - nextflow.nextflow                      # Nextflow syntax highlighting
     - oderwat.indent-rainbow                 # Highlight indentation level
     - streetsidesoftware.code-spell-checker  # Spelling checker for source code

.nf-core.yml

@@ -0,0 +1 @@
+repository_type: pipeline