Merge pull request #36 from mskcc/test_profile_run

PR for MVP release! (for real)

.editorconfig

@@ -31,6 +31,7 @@ indent_size = unset
 # ignore Readme
 [README.md]
 indent_style = unset
+trim_trailing_whitespace = unset
 
 # ignore python
 [*.{py,md}]

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,53 +2,53 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-- type: textarea
-  id: description
-  attributes:
-    label: Description of the bug
-    description: A clear and concise description of what the bug is.
-  validations:
-    required: true
-- type: textarea
-  id: command_used
-  attributes:
-    label: Command used and terminal output
-    description: Steps to reproduce the behaviour. Please paste the command you used
-      to launch the pipeline and the output from your terminal.
-    render: console
-    placeholder: '$ nextflow run ...
-
-
-      Some output where something broke
-
-      '
-- type: textarea
-  id: files
-  attributes:
-    label: Relevant files
-    description: 'Please drag and drop the relevant files here. Create a `.zip` archive
-      if the extension is not allowed.
-
-      Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-      in the directory where you launched the pipeline)_ as well as custom Nextflow
-      configuration files.
-
-      '
-- type: textarea
-  id: system
-  attributes:
-    label: System information
-    description: '* Nextflow version _(eg. 23.04.0)_
-
-      * Hardware _(eg. HPC, Desktop, Cloud)_
-
-      * Executor _(eg. slurm, local, awsbatch)_
-
-      * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
-      or Apptainer)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of mskcc/neoantigenpipeline _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: "$ nextflow run ...
+
+
+        Some output where something broke
+
+        "
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
+
+        "
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: "* Nextflow version _(eg. 23.04.0)_
+
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+
+        * Executor _(eg. slurm, local, awsbatch)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
+        or Apptainer)_
+
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
+        * Version of mskcc/neoantigenpipeline _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.gitignore

@@ -6,3 +6,6 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test/
+out/*
+.nf-test.log

.nf-core.yml

@@ -1,23 +1,23 @@
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-neoantigenpipeline_logo_light.png
-  - docs/images/nf-core-neoantigenpipeline_logo_light.png
-  - docs/images/nf-core-neoantigenpipeline_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-neoantigenpipeline_logo_light.png
+    - docs/images/nf-core-neoantigenpipeline_logo_light.png
+    - docs/images/nf-core-neoantigenpipeline_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
   files_unchanged:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-neoantigenpipeline_logo_light.png
-  - docs/images/nf-core-neoantigenpipeline_logo_light.png
-  - docs/images/nf-core-neoantigenpipeline_logo_dark.png
-  - .github/ISSUE_TEMPLATE/bug_report.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-neoantigenpipeline_logo_light.png
+    - docs/images/nf-core-neoantigenpipeline_logo_light.png
+    - docs/images/nf-core-neoantigenpipeline_logo_dark.png
+    - .github/ISSUE_TEMPLATE/bug_report.yml
   multiqc_config:
-  - report_comment
+    - report_comment
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
+    - manifest.name
+    - manifest.homePage
 repository_type: pipeline
 template:
   prefix: mskcc

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+README.md