Merge branch 'main' of https://github.com/CCBR/RENEE

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,25 @@
+## Changes
+
+<!--
+Provide a summary of what is included in this Pull Request (PR).
+-->
+
+## Issues
+
+<!--
+Reference any issues related to this PR.
+If this PR fixes any issues, [use a keyword](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword)
+when referring to the issue.
+-->
+
+<!--
+**Reviewers**: Use the @ feature to mention anyone responsible for reviewing/completing this request.
+-->
+
+## PR Checklist
+
+(~Strikethrough~ any points that are not applicable.)
+
+- [ ] This comment contains a description of changes with justifications, with any relevant issues linked.
+- [ ] Update docs if there are any API changes.
+- [ ] Update `CHANGELOG.md` with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

.pre-commit-config.yaml

@@ -1,11 +1,24 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html|
+      ^_extensions/
+   )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
       - id: check-added-large-files
-      #- id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        # https://github.com/codespell-project/codespell/issues/1498
   # Python formatting
   - repo: https://github.com/psf/black
     rev: 23.7.0
@@ -21,13 +34,14 @@ repos:
     rev: v2.7.1
     hooks:
       - id: prettier
-  # spell check
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
-    hooks:
-      - id: codespell
   # enforce commit format
   - repo: https://github.com/compilerla/conventional-pre-commit
     rev: v2.3.0
     hooks:
       - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
+  - repo: https://github.com/citation-file-format/cffconvert
+    rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
+    hooks:
+      - id: validate-cff

.prettierignore

@@ -0,0 +1,9 @@
+# gitignore
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+*.code-workspace
+assets/*.html
+_extensions

.prettierrc

@@ -0,0 +1,4 @@
+overrides:
+    - files: "*.md"
+      options:
+          tabWidth: 2

CHANGELOG.md

@@ -1,5 +1,7 @@
 ## development version
 
+## v2.5.9
+
 - Fix bugs that prevented single-end data from running through the pipeline. (#58, @kelly-sovacool)
 - Increase wall time for kraken and bbmerge rules. (#68, @slsevilla)
 

VERSION

@@ -1 +1 @@
-2.5.8
+2.5.9-dev

resources/cluster.json

@@ -10,8 +10,8 @@
         "error": "logfiles/slurmfiles/${{SLURM_JOBID}}.%j.{rule}.{wildcards}.err"
     },
     "bbmerge": {
-        "mem": "64g"
-	"time": "1-00:00:00"
+        "mem": "64g",
+        "time": "1-00:00:00"
     },
     "fastqc": {
         "threads": "32",
@@ -28,13 +28,13 @@
     "kraken_pe": {
         "cpus-per-task": "32",
         "gres": "lscratch:256",
-        "mem": "110g"
+        "mem": "110g",
         "time": "1-00:00:00"
     },
     "kraken_se": {
         "cpus-per-task": "32",
         "gres": "lscratch:256",
-        "mem": "110g"
+        "mem": "110g",
         "time": "1-00:00:00"
     },
     "pca": {