Merge pull request #19 from sunbeam-labs/18-hotfixes-for-new-containe…

…rization-and-versioning

18 hotfixes for new containerization and versioning

.github/workflows/release.yml

@@ -54,14 +54,14 @@ jobs:
             - name: Log in to Docker Hub
               uses: docker/login-action@v3
               with:
-                username: ${{ secrets.DOCKER_USERNAME }}
-                password: ${{ secrets.DOCKER_PASSWORD }}
+                username: ${{ secrets.DOCKERHUB_USERNAME }}
+                password: ${{ secrets.DOCKERHUB_TOKEN }}
 
             - name: Extract metadata (tags, labels) for Docker
               id: meta
               uses: docker/metadata-action@v5
               with:
-                images: ctbushman/sbx_mapping
+                images: sunbeam-labs/sbx_mapping
 
             - name: Build and push Docker image
               uses: docker/build-push-action@v5
@@ -75,6 +75,7 @@ jobs:
     test-apptainer:
       name: Apptainer Test
       runs-on: ubuntu-latest
+      needs: build-and-push-to-dockerhub
 
       steps:
         - name: Checkout Code

VERSION

@@ -1 +1 @@
-0.0.0
+0.0.1

sbx_mapping.smk

@@ -1,6 +1,20 @@
 # -*- mode: Snakemake -*-
 
 import sys
+import os
+from pathlib import Path
+
+
+def get_mapping_path() -> Path:
+    for fp in sys.path:
+        if fp.split("/")[-1] == "sbx_mapping":
+            return Path(fp)
+    raise Error(
+        "Filepath for sbx_mapping not found, are you sure it's installed under extensions/sbx_mapping?"
+    )
+
+
+SBX_MAPPING_VERSION = open(get_mapping_path() / "VERSION").read().strip()
 
 try:
     GenomeFiles
@@ -79,7 +93,7 @@ rule build_genome_index:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     shell:
         "cd {Cfg[sbx_mapping][genomes_fp]} && bwa index {input} 2>&1 | tee {log}"
 
@@ -100,7 +114,7 @@ rule align_to_genome:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     shell:
         """
         bwa mem -M -t {threads} \
@@ -124,7 +138,7 @@ rule samtools_convert:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     shell:
         """
         samtools view -@ {threads} -b {Cfg[sbx_mapping][samtools_opts]} {input} 2>&1 | tee {log.view_log} | \
@@ -143,7 +157,7 @@ rule filter_aln_quality:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     script:
         "scripts/filter_aln_quality.py"
 
@@ -160,7 +174,7 @@ rule samtools_index:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     shell:
         "samtools index {input} {output} 2>&1 | tee {log}"
 
@@ -183,7 +197,7 @@ rule get_sliding_coverage:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     script:
         "scripts/get_sliding_coverage.py"
 
@@ -222,7 +236,7 @@ rule get_coverage_filtered:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     script:
         "scripts/samtools_get_coverage.py"
 
@@ -252,7 +266,7 @@ rule summarize_num_mapped_reads:
     conda:
         "envs/sbx_mapping_env.yml"
     container:
-        "docker://ctbushman/sbx_mapping:0.0.0"
+        f"docker://sunbeam-labs/sbx_mapping:{SBX_MAPPING_VERSION}"
     shell:
         """
         samtools idxstats {input} | (sed 's/^/{wildcards.sample}\t/') > {output}

scripts/filter_aln_quality.py

@@ -1,3 +1,4 @@
+# from scripts.filter_aln_quality_f import filter_bam_alignments
 import pysam
 import re