nf-core · ewels · Mar 19, 2021 · Mar 19, 2021 · Mar 19, 2021 · Mar 22, 2021
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -4,6 +4,8 @@ on: [push, pull_request]
 jobs:
   MakeTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_VER: 21.03.0-edge
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -22,21 +24,32 @@ jobs:
         env:
           CAPSULE_LOG: none
         run: |
-          mkdir /tmp/nextflow
-          cd /tmp/nextflow
           wget -qO- get.nextflow.io | bash
-          sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+          sudo mv nextflow /usr/local/bin/
 
-      - name: Run nf-core/tools
-        run: |
-          nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
-          nf-core --log-file log.txt lint nf-core-testpipeline --fail-ignored
-          nf-core --log-file log.txt list
-          nf-core --log-file log.txt licences nf-core-testpipeline
-          nf-core --log-file log.txt sync nf-core-testpipeline/
-          nf-core --log-file log.txt schema build nf-core-testpipeline/ --no-prompts
-          nf-core --log-file log.txt bump-version nf-core-testpipeline/ 1.1
-          nf-core --log-file log.txt modules install nf-core-testpipeline/ --tool fastqc
+      - name: nf-core create
+        run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
+
+      - name: nf-core lint
+        run: nf-core --log-file log.txt lint nf-core-testpipeline --fail-ignored
+
+      - name: nf-core list
+        run: nf-core --log-file log.txt list
+
+      - name: nf-core licences
+        run: nf-core --log-file log.txt licences nf-core-testpipeline
+
+      - name: nf-core sync
+        run: nf-core --log-file log.txt sync nf-core-testpipeline/
+
+      - name: nf-core schema
+        run: nf-core --log-file log.txt schema build nf-core-testpipeline/ --no-prompts
+
+      - name: nf-core bump-version
+        run: nf-core --log-file log.txt bump-version nf-core-testpipeline/ 1.1
+
+      - name: nf-core modules install
+        run: nf-core --log-file log.txt modules install nf-core-testpipeline/ --tool fastqc
 
       - name: Upload log file artifact
         if: ${{ always() }}

diff --git a/.github/workflows/markdown-lint.yml b/.github/workflows/markdown-lint.yml
@@ -16,3 +16,28 @@ jobs:
 
       - name: Run Markdownlint
         run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Markdown linting is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install `markdownlint-cli`
+                * On Mac: `brew install markdownlint-cli`
+                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli): `npm install -g markdownlint-cli`
+            * Try to automatically fix errors in your pipeline: `markdownlint . --config .github/markdownlint.yml --fix`
+            * Check that there are no remaining problems: `markdownlint . --config .github/markdownlint.yml`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
diff --git a/.github/workflows/python-lint.yml b/.github/workflows/python-lint.yml
@@ -15,3 +15,25 @@ jobs:
 
       - name: Check code lints with Black
         uses: jpetrucciani/black-check@master
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            ## Python linting (`black`) is failing
+
+            To keep the code consistent with lots of contributors, we run automated code consistency checks.
+            To fix this CI test, please run:
+
+            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+            * Fix formatting errors in your pipeline: `black .`
+
+            Once you push these changes the test should pass, and you can hide this comment :+1:
+
+            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+            Thanks again for your contribution!
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          allow-repeats: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,12 @@
 # nf-core/tools: Changelog
 
-## v1.14dev
+## v1.13.2dev
 
-_..nothing yet.._
+### Tools code
+
+* Fix `UnicodeDecodeError` with `nf-core create` on some systems [[#931]](https://github.com/nf-core/tools/issues/931)
+* Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read
+* Added automated PR comments to the Markdownlint and Python Black lint CI tests to explain failures
 
 ## [v1.13.1 - Copper Crocodile Patch :crocodile: :pirate_flag:](https://github.com/nf-core/tools/releases/tag/1.13.1) - [2021-03-19]
 

diff --git a/docs/api/_src/_static/css/custom.css b/docs/api/_src/_static/css/custom.css
@@ -0,0 +1,199 @@
+@media (prefers-color-scheme: light) {
+	.wy-nav-side{
+		background-color: #ededed;
+	}
+	.wy-nav-top, .wy-side-nav-search, .wy-menu-vertical a:active {
+		background-color: #32AD65;
+	}
+	.wy-menu-vertical a{
+		color: #343434;
+	}
+	.wy-menu-vertical a:hover{
+		background-color: #abacab85;
+	}
+	.wy-menu-vertical header, .wy-menu-vertical p.caption {
+		color:#32AD65;
+	}
+
+	.wy-side-nav-search input[type=text]{
+		border: none;
+	}
+
+	code, .rst-content code.literal{
+		background-color: rgba(220,220,220,0.4);
+		color: #db9444;
+		border: none;
+	}
+	.rst-content .note .admonition-title{
+		background-color: #72757bfc
+	}
+
+	html.writer-html4 .rst-content dl:not(.docutils)>dt, html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)>dt {
+		background-color: #32AD65;
+		border:none;
+	}
+	.rst-content .method>dt>code {
+		color: #f5f6f7;
+	}
+	.sig-paren{
+		color: #db9444;
+	}
+	.rst-content div[class^=highlight], .rst-content pre.literal-block{
+		border:none;
+	}
+    .highlight{
+        background-color: #242424;
+        color: #e5e6e7;
+	}
+	.highlight .hll{
+		color: #e5e6e7;
+		background-color: #585b60fc;
+	}
+	.highlight .k, .highlight .nt, .highlight .no{
+		color: #6fb2e8;
+	}
+	.highlight .s, .highlight .s1, .highlight .s2{
+		color: #32AD65;
+	}
+	.highlight .nb, .highlight .o{
+		color: #db9444;
+	}
+	.highlight .c1{
+		color: #88898afc;
+	}
+	.highlight .nv{
+		color: #f9d977;
+	}
+	.btn.btn-neutral {
+		background-color: #e5e6e7d4 !important;	
+	}
+    .rst-content .hint .admonition-title, .rst-content .hint .wy-alert-title, .rst-content .important .admonition-title, .rst-content .important .wy-alert-title, .rst-content .tip .admonition-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .admonition-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .wy-alert.wy-alert-success .wy-alert-title{
+		background-color: #32AD65;
+		color: #e5e6e7;
+	}
+
+	.rst-content .note, .rst-content .seealso, .rst-content .wy-alert-info.admonition, .rst-content .wy-alert-info.admonition-todo, .rst-content .wy-alert-info.attention, .rst-content .wy-alert-info.caution, .rst-content .wy-alert-info.danger, .rst-content .wy-alert-info.error, .rst-content .wy-alert-info.hint, .rst-content .wy-alert-info.important, .rst-content .wy-alert-info.tip, .rst-content .wy-alert-info.warning, .wy-alert.wy-alert-info,
+    .rst-content .hint, .rst-content .important, .rst-content .tip, .rst-content .wy-alert-success.admonition, .rst-content .wy-alert-success.admonition-todo, .rst-content .wy-alert-success.attention, .rst-content .wy-alert-success.caution, .rst-content .wy-alert-success.danger, .rst-content .wy-alert-success.error, .rst-content .wy-alert-success.note, .rst-content .wy-alert-success.seealso, .rst-content .wy-alert-success.warning, .wy-alert.wy-alert-success{
+	color: #343434;
+	background-color: #e3e3e3;
+	border: none;
+	}
+
+
+.rst-content .admonition-todo .admonition-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .attention .admonition-title, .rst-content .attention .wy-alert-title, .rst-content .caution .admonition-title, .rst-content .caution .wy-alert-title, .rst-content .warning .admonition-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.admonition .admonition-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .wy-alert.wy-alert-warning .wy-alert-title {
+		background-color: #f4a25b;
+	}
+.rst-content .admonition-todo, .rst-content .attention, .rst-content .caution, .rst-content .warning, .rst-content .wy-alert-warning.admonition, .rst-content .wy-alert-warning.danger, .rst-content .wy-alert-warning.error, .rst-content .wy-alert-warning.hint, .rst-content .wy-alert-warning.important, .rst-content .wy-alert-warning.note, .rst-content .wy-alert-warning.seealso, .rst-content .wy-alert-warning.tip, .wy-alert.wy-alert-warning {
+    color: #343434;
+	background-color: #e3e3e3;
+	}
+
+
+}
+@media (prefers-color-scheme: dark) {
+	.wy-nav-content-wrap {
+		background-color: #181a1b
+	}
+	.wy-nav-top, .wy-side-nav-search, .wy-menu-vertical a:active {
+		background-color: #32AD65;
+	}
+	.wy-menu-vertical header, .wy-menu-vertical p.caption {
+		color:#32AD65;
+	}
+	.wy-nav-side{
+		background-color: #2E2E2E;
+	}
+	.wy-nav-content{
+		background-color: #343434;
+		color: #e5e6e7;
+	}
+	a, a:hover, a:focus, a:active {
+		color: #6fb2e8;
+	}
+	code, .rst-content code.literal{
+		background-color: rgba(220,220,220,0.1);
+		color: #db9444;
+		border: none;
+	}
+	.wy-side-nav-search input[type=text]{
+		border: none;
+		background-color: #e5e6e7;
+	}
+	.wy-side-nav-search>div.version{
+		color: #e5e6e7c9;
+	}
+	.wy-side-nav-search .wy-dropdown>a, .wy-side-nav-search>a {
+		color: #e5e6e7;
+	}
+
+	html.writer-html4 .rst-content dl:not(.docutils)>dt, html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)>dt {
+		background-color: #32AD65;
+		border:none;
+	}
+	html.writer-html4 .rst-content dl:not(.docutils) dl:not(.field-list)>dt, html.writer-html5 .rst-content dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple) dl:not(.field-list)>dt{
+		background-color:#777;
+		color:#e5e6e7a6;
+	}
+	.rst-content code {
+		color: #e5e6e7d4;
+	}
+	.rst-content .method>dt>code {
+		color: #e5e6e7;
+	}
+	.sig-paren{
+		color: #db9444;
+	}
+	.rst-content .note .admonition-title{
+		background-color: #72757bfc
+	}
+	.rst-content div[class^=highlight], .rst-content pre.literal-block{
+		border:none;
+	}
+
+    .highlight{
+        background-color: #242424;
+        color: #e5e6e7;
+	}
+	.highlight .hll{
+		color: #e5e6e7;
+		background-color: #585b60fc;
+	}
+	.highlight .k, .highlight .nt, .highlight .no{
+		color: #6fb2e8;
+	}
+	.highlight .s, .highlight .s1, .highlight .s2{
+		color: #32AD65;
+	}
+	.highlight .nb, .highlight .o{
+		color: #db9444;
+	}
+	.highlight .c1{
+		color: #88898afc;
+	}
+	.highlight .nv{
+		color: #f9d977;
+	}
+	.btn.btn-neutral {
+		background-color: #e5e6e7d4 !important;	
+	}
+
+    .rst-content .hint .admonition-title, .rst-content .hint .wy-alert-title, .rst-content .important .admonition-title, .rst-content .important .wy-alert-title, .rst-content .tip .admonition-title, .rst-content .tip .wy-alert-title, .rst-content .wy-alert-success.admonition-todo .admonition-title, .rst-content .wy-alert-success.admonition-todo .wy-alert-title, .rst-content .wy-alert-success.admonition .admonition-title, .rst-content .wy-alert-success.admonition .wy-alert-title, .rst-content .wy-alert-success.attention .admonition-title, .rst-content .wy-alert-success.attention .wy-alert-title, .rst-content .wy-alert-success.caution .admonition-title, .rst-content .wy-alert-success.caution .wy-alert-title, .rst-content .wy-alert-success.danger .admonition-title, .rst-content .wy-alert-success.danger .wy-alert-title, .rst-content .wy-alert-success.error .admonition-title, .rst-content .wy-alert-success.error .wy-alert-title, .rst-content .wy-alert-success.note .admonition-title, .rst-content .wy-alert-success.note .wy-alert-title, .rst-content .wy-alert-success.seealso .admonition-title, .rst-content .wy-alert-success.seealso .wy-alert-title, .rst-content .wy-alert-success.warning .admonition-title, .rst-content .wy-alert-success.warning .wy-alert-title, .rst-content .wy-alert.wy-alert-success .admonition-title, .wy-alert.wy-alert-success .rst-content .admonition-title, .wy-alert.wy-alert-success .wy-alert-title{
+		background-color: #32AD65;
+		color: #e5e6e7;
+	}
+
+	.rst-content .note, .rst-content .seealso, .rst-content .wy-alert-info.admonition, .rst-content .wy-alert-info.admonition-todo, .rst-content .wy-alert-info.attention, .rst-content .wy-alert-info.caution, .rst-content .wy-alert-info.danger, .rst-content .wy-alert-info.error, .rst-content .wy-alert-info.hint, .rst-content .wy-alert-info.important, .rst-content .wy-alert-info.tip, .rst-content .wy-alert-info.warning, .wy-alert.wy-alert-info,
+    .rst-content .hint, .rst-content .important, .rst-content .tip, .rst-content .wy-alert-success.admonition, .rst-content .wy-alert-success.admonition-todo, .rst-content .wy-alert-success.attention, .rst-content .wy-alert-success.caution, .rst-content .wy-alert-success.danger, .rst-content .wy-alert-success.error, .rst-content .wy-alert-success.note, .rst-content .wy-alert-success.seealso, .rst-content .wy-alert-success.warning, .wy-alert.wy-alert-success{
+	color: #343434;
+	background-color: #e3e3e3;
+	border: none;
+	}
+
+    .rst-content .admonition-todo .admonition-title, .rst-content .admonition-todo .wy-alert-title, .rst-content .attention .admonition-title, .rst-content .attention .wy-alert-title, .rst-content .caution .admonition-title, .rst-content .caution .wy-alert-title, .rst-content .warning .admonition-title, .rst-content .warning .wy-alert-title, .rst-content .wy-alert-warning.admonition .admonition-title, .rst-content .wy-alert-warning.admonition .wy-alert-title, .rst-content .wy-alert-warning.danger .admonition-title, .rst-content .wy-alert-warning.danger .wy-alert-title, .rst-content .wy-alert-warning.error .admonition-title, .rst-content .wy-alert-warning.error .wy-alert-title, .rst-content .wy-alert-warning.hint .admonition-title, .rst-content .wy-alert-warning.hint .wy-alert-title, .rst-content .wy-alert-warning.important .admonition-title, .rst-content .wy-alert-warning.important .wy-alert-title, .rst-content .wy-alert-warning.note .admonition-title, .rst-content .wy-alert-warning.note .wy-alert-title, .rst-content .wy-alert-warning.seealso .admonition-title, .rst-content .wy-alert-warning.seealso .wy-alert-title, .rst-content .wy-alert-warning.tip .admonition-title, .rst-content .wy-alert-warning.tip .wy-alert-title, .rst-content .wy-alert.wy-alert-warning .admonition-title, .wy-alert.wy-alert-warning .rst-content .admonition-title, .wy-alert.wy-alert-warning .wy-alert-title {
+		background-color: #f4a25b;
+	}
+    .rst-content .admonition-todo, .rst-content .attention, .rst-content .caution, .rst-content .warning, .rst-content .wy-alert-warning.admonition, .rst-content .wy-alert-warning.danger, .rst-content .wy-alert-warning.error, .rst-content .wy-alert-warning.hint, .rst-content .wy-alert-warning.important, .rst-content .wy-alert-warning.note, .rst-content .wy-alert-warning.seealso, .rst-content .wy-alert-warning.tip, .wy-alert.wy-alert-warning {
+    color: #343434;
+	background-color: #e3e3e3;
+	}
+}
diff --git a/docs/api/_src/conf.py b/docs/api/_src/conf.py
@@ -14,9 +14,9 @@
 #
 import os
 import sys
-import nf_core
 
 sys.path.insert(0, os.path.abspath("../../../nf_core"))
+import nf_core
 
 # -- Project information -----------------------------------------------------
 
@@ -90,6 +90,10 @@
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
+html_css_files = [
+    "css/custom.css",
+]
+
 #
 # The default sidebars (for documents that don't match any pattern) are
 # defined by theme itself.  Builtin themes are using these templates by