chore: Merge branch 'main' into cleanup

remove fastqvalidator container -- unused

CHANGELOG.md

@@ -1,7 +1,11 @@
 ## XAVIER development version
-- Bug fixes:
-  - Fix minor bug in assess_significance.R script associated with rule freec_exome_somatic (#120, @samarth8392)
-
+
+## XAVIER 3.1.2
+
+- Fix minor bug in `assess_significance.R` script associated with rule `freec_exome_somatic`. (#120, @samarth8392)
+- Fix bug in multiqc docker container, which caused an error when running xavier from ccbrpipeliner/7. (#123, @kelly-sovacool)
+- Fix `cache` subcommand to correctly read the container images config file. (#124, @kelly-sovacool)
+
 ## XAVIER 3.1.1
 
 - New contributing guide available on GitHub and the documentation website. (#114, @kelly-sovacool)

CITATION.cff

@@ -46,5 +46,5 @@ identifiers:
   - description: Archived snapshots of all versions
     type: doi
     value: 10.5281/zenodo.12727315
-version: v3.1.1
-date-released: "2024-10-02"
+version: v3.1.2
+date-released: "2024-11-05"

VERSION

@@ -1 +1 @@
-3.1.1-dev
+3.1.2-dev

config/containers/images.json

@@ -7,7 +7,7 @@
         "fastqc": "docker://nciccbr/ccbr_fastqc_0.11.9:v1.1",
         "fastqvalidator": "docker://nciccbr/ccbr_fastqvalidator:v0.1.0",
         "kraken": "docker://nciccbr/ccbr_kraken_v2.1.1:v0.0.1",
-        "multiqc": "docker://nciccbr/ccbr_multiqc_1.15:v1",
+        "multiqc": "docker://nciccbr/ccbr_multiqc_1.15:v2",
         "picard": "docker://nciccbr/ccbr_picard:v0.0.1",
         "python": "docker://nciccbr/ccbr_python:v0.0.1",
         "qualimap": "docker://nciccbr/ccbr_qualimap:v0.0.1"

src/xavier/__main__.py

@@ -92,8 +92,7 @@ def cache(sub_args):
 
     sif_cache = sub_args.sif_cache
     # Get absolute PATH to templates in XAVIER git repo
-    repo_path = os.path.dirname(os.path.abspath(__file__))
-    images = os.path.join(repo_path, "config", "containers", "images.json")
+    images = xavier_base("config", "containers", "images.json")
 
     # Create image cache
     if not exists(sif_cache):
@@ -135,7 +134,7 @@ def cache(sub_args):
             # Quote user provided values to avoid shell injections
             masterjob = subprocess.Popen(
                 "sbatch --parsable -J pl:cache --gres=lscratch:200  --time=10:00:00 --mail-type=BEGIN,END,FAIL "
-                + str(os.path.join(repo_path, "resources", "cacher"))
+                + xavier_base("resources", "cacher")
                 + " slurm "
                 + " -s '{}' ".format(sif_cache)
                 + " -i '{}' ".format(",".join(pull))