chore: new release

.github/copilot-instructions.md

@@ -64,17 +64,22 @@ cd docs && make html
 ### Adding a New Rule
 ```snakemake
 rule my_rule:
-    conda:
-        getCondaEnv("python3.yaml")
+    """
+    Documentation of my_rule goes here. Describe inputs, outputs, and purpose.
+    """
     input:
         script=getScript("mydir/myscript.py"),
         data=lambda wc: config["assignments"][wc.assignment]["design_file"],
     output:
         "results/assignment/{assignment}/myoutput.tsv",
     log:
         "results/logs/assignment/my_rule.{assignment}.log",
+    conda:
+        getCondaEnv("python3.yaml")
     shell:
-        "python {input.script} --input {input.data} > {output} 2> {log}"
+        """
+        python {input.script} --input {input.data} >{output} 2>{log}
+        """
 ```
 
 ### Config Access

.github/release-please-config.json

@@ -11,7 +11,64 @@
             "draft": false,
             "prerelease": true,
             "tag-prefix": "v",
-            "include-component-in-tag": false
+            "include-component-in-tag": false,
+            "changelog-sections": [
+                {
+                    "type": "feat",
+                    "section": "Features",
+                    "hidden": false
+                },
+                {
+                    "type": "fix",
+                    "section": "Bug Fixes",
+                    "hidden": false
+                },
+                {
+                    "type": "perf",
+                    "section": "Performance Improvements",
+                    "hidden": false
+                },
+                {
+                    "type": "revert",
+                    "section": "Reverts",
+                    "hidden": false
+                },
+                {
+                    "type": "docs",
+                    "section": "Documentation",
+                    "hidden": false
+                },
+                {
+                    "type": "style",
+                    "section": "Styles",
+                    "hidden": true
+                },
+                {
+                    "type": "chore",
+                    "section": "Miscellaneous Chores",
+                    "hidden": true
+                },
+                {
+                    "type": "refactor",
+                    "section": "Code Refactoring",
+                    "hidden": true
+                },
+                {
+                    "type": "test",
+                    "section": "Tests",
+                    "hidden": true
+                },
+                {
+                    "type": "build",
+                    "section": "Build System",
+                    "hidden": true
+                },
+                {
+                    "type": "ci",
+                    "section": "Continuous Integration",
+                    "hidden": true
+                }
+            ]
         }
     }
 }

.pre-commit-config.yaml

@@ -43,7 +43,7 @@ repos:
 
 ci:
   autofix_commit_msg: |
-    [pre-commit.ci] auto fixes from pre-commit hooks
+    ci: auto fixes from pre-commit hooks
 
     for more information, see https://pre-commit.ci
   autofix_prs: true

config/example_assignment_bbmap.yaml

@@ -1,5 +1,5 @@
 ---
-version: "0.6"
+version: "0.7"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15
@@ -8,14 +8,15 @@ assignments:
       tool: bbmap
       configs:
         min_mapping_quality: 30 # 30 is default for bbmap
-        sequence_length: 171 # sequence length of design excluding adapters.
-        alignment_start: 1 # start of an alignment in the reference/design_file.
     FWD:
       - resources/Assignment_BasiC/R1.fastq.gz
     BC:
       - resources/Assignment_BasiC/R2.fastq.gz
     REV:
       - resources/Assignment_BasiC/R3.fastq.gz
     design_file: resources/design.fa
+    design_check:
+      sequence_start: 1 # start of an alignment in the reference/design_file.
+      sequence_length: 171 # sequence length of design excluding adapters.
     configs:
       default: {} # name of an example filtering config

config/example_assignment_bwa.yaml

@@ -1,5 +1,5 @@
 ---
-version: "0.6"
+version: "0.7"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15

config/example_assignment_exact_lazy.yaml

@@ -1,5 +1,5 @@
 ---
-version: "0.6"
+version: "0.7"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15

config/example_assignment_exact_linker.yaml

@@ -1,5 +1,5 @@
 ---
-version: "0.6"
+version: "0.7"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 20

config/example_assignment_pbmm2.yaml

@@ -1,18 +1,19 @@
 ---
-version: "0.6"
+version: "0.7"
 
 assignments:
   exampleLongRead:
     bc_length: 15
     long_read_input: resources/long_read/CEBPRE_10k.bam
     design_file: resources/long_read/CEBPRE_reference.fasta
+    design_check:
+      sequence_start: 1
+      sequence_length: 303
     alignment_tool:
       tool: pbmm2
       configs:
         preset: SUBREAD
         min_concordance: 0.9
-        alignment_start: 1
-        sequence_length: 303
     linker: GCAAAGTGAACACATCGCTAAGCGAAAGCTAAG # linker sequence in the read after we expect the BC
     configs:
       test:

config/example_config.yaml

@@ -1,5 +1,5 @@
 ---
-version: "0.6"
+version: "0.7"
 assignments:
   exampleAssignment: # name of an example assignment (can be any string)
     bc_length: 15

config/example_count.yaml

@@ -1,5 +1,5 @@
 ---
-version: "0.6"
+version: "0.7"
 experiments:
   exampleCount:
     bc_length: 15