Merge pull request #2 from sunbeam-labs/1-remove-dependency-on-deprecated-sunbeamlib-feature

Move envs to envs/ and add missing parse_blast6 function

Author: Ulthran

.github/workflows/conda_env_check.yml

@@ -0,0 +1,27 @@
+name: Check Conda Envs
+
+on:
+  pull_request:
+    branches: [ main, master ]
+  push:
+    branches: [ main, master ]
+  workflow_dispatch:
+    inputs:
+      envs:
+        description: 'Regex for envs'     
+        required: false
+        default: 'envs/'
+
+jobs:
+  check_conda_envs:
+    name: Check Conda Envs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+      
+      - name: Check Conda Envs
+        uses: Ulthran/conda_env_check@v1
+        with:
+          envs: "envs/"

.github/workflows/tests.yml

@@ -18,12 +18,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Test with Sunbeam
-        uses: sunbeam-labs/sbx_test_action@v0
-        with:
-          sunbeam-version: 'dev'
-          install-options: '-m'
-          extension-name: 'sunbeam-labs/sbx_assembly'
-          extension-branch-name: ${{ github.head_ref }}
+        uses: sunbeam-labs/sbx_test_action@v1
 
       - name: Dump Logs
         shell: bash

LICENSE

@@ -54,7 +54,7 @@ rule build_diamond_db:
     log:
         LOG_FP / "build_diamond_db.log",
     conda:
-        "sbx_annotation.yml"
+        "envs/sbx_annotation.yml"
     shell:
         """
         diamond makedb --in {input} -d {input} 2>&1 | tee {log}
@@ -75,7 +75,7 @@ rule run_blastn:
         db=lambda wildcard: Blastdbs["nucl"][wildcard.db],
     threads: Cfg["sbx_annotation"]["threads"]
     conda:
-        "sbx_annotation.yml"
+        "envs/sbx_annotation.yml"
     shell:
         """
         blastn \
@@ -103,7 +103,7 @@ rule run_diamond_blastp:
         LOG_FP / "run_diamond_blastp_{db}_{orf_finder}_{sample}.log",
     threads: Cfg["sbx_annotation"]["threads"]
     conda:
-        "sbx_annotation.yml"
+        "envs/sbx_annotation.yml"
     shell:
         """
         if [ -s {input.genes} ]; then
@@ -136,7 +136,7 @@ rule run_diamond_blastx:
         LOG_FP / "run_diamond_blastx_{db}_{orf_finder}_{sample}.log",
     threads: Cfg["sbx_annotation"]["threads"]
     conda:
-        "sbx_annotation.yml"
+        "envs/sbx_annotation.yml"
     shell:
         """
         if [ -s {input.genes} ]; then
@@ -166,7 +166,7 @@ rule blast_report:
     output:
         ANNOTATION_FP / "{blast_prog}" / "{db}" / "{query}" / "report.tsv",
     conda:
-        "sbx_annotation.yml"
+        "envs/sbx_annotation.yml"
     script:
         "scripts/blast_report.py"
 
@@ -212,7 +212,7 @@ rule aggregate_results:
         nucl=Blastdbs["nucl"],
         prot=Blastdbs["prot"],
     conda:
-        "sbx_annotation.yml"
+        "envs/sbx_annotation.yml"
     script:
         "scripts/aggregate_results.py"