Merge branch 'dev' into feat/hello-seqera

nextflow-io · Oct 27, 2024 · 6b6f95b · 6b6f95b
2 parents ff0a41d + 7bda265
commit 6b6f95b
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Showing 25 changed files with 524,683 additions and 152 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,10 +1,14 @@
 {
     "name": "nfcore",
-    "image": "nfcore/gitpod:latest",
+    "image": "ghcr.io/nextflow-io/training:latest",
     "remoteUser": "gitpod",
-
-    "postCreateCommand": "pre-commit install --install-hooks",
-
+    "features": {
+        "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
+    },
+    "remoteEnv": {
+        "NXF_HOME": "/workspaces/.nextflow",
+        "HOST_PROJECT_PATH": "${localWorkspaceFolder}"
+    },
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
@@ -13,12 +17,13 @@
             "settings": {
                 "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
-
             // Add the IDs of extensions you want installed when the container is created.
             "extensions": [
                 "ms-python.python",
                 "ms-python.vscode-pylance",
-                "nf-core.nf-core-extensionpack"
+                "nf-core.nf-core-extensionpack",
+                "nextflow.nextflow",
+                "codezombiech.gitignore",
             ]
         }
     },

diff --git a/docs/hello_nextflow/05_hello_operators.md b/docs/hello_nextflow/05_hello_operators.md
@@ -411,7 +411,6 @@ Let's write a new process to define how that's going to work, based on the comma
 process GATK_GENOMICSDB {
 
     container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
-
     publishDir 'results_genomics', mode: 'copy'
 
     input:
@@ -736,8 +735,8 @@ _Before:_
 
 ```groovy title="hello-operators.nf" linenums="78"
 input:
-    path all_gvcfs_ch
-    path all_idxs_ch
+    path all_gvcfs
+    path all_idxs
     path interval_list
     val cohort_name
 ```
@@ -746,8 +745,8 @@ _After:_
 
 ```groovy title="hello-operators.nf" linenums="78"
 input:
-    path all_gvcfs_ch
-    path all_idxs_ch
+    path all_gvcfs
+    path all_idxs
     path interval_list
     val cohort_name
     path ref_fasta