Merge pull request #11 from cokelaer/main

hotfix to use on HPC clusters

README.rst

@@ -109,6 +109,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.1.1     * hotfix for running on HPC (slurm)
 1.1.0     * Uses click (refactoring of sequana_pipetools)
 1.0.1     * add sequana_wrappers in the config/pipeline
 1.0.0     * use graphviz apptainer and latest wrappers

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-ribofinder"
-version = "1.1.0"
+version = "1.1.1"
 description = "A multi-sample identification of ribosomal content"
 authors = ["Sequana Team"]
 license = "BSD-3"

sequana_pipelines/ribofinder/__init__.py

@@ -1,6 +1,11 @@
-import pkg_resources
-try:
-    version = pkg_resources.require("sequana_ribofinder")[0].version
-except:
-    version = ">=0.8.0"
+import importlib.metadata as metadata
+
+def get_package_version(package_name):
+    try:
+        version = metadata.version(package_name)
+        return version
+    except metadata.PackageNotFoundError:
+        return f"{package_name} not found"
+
+version = get_package_version("sequana-ribofinder")
 

sequana_pipelines/ribofinder/ribofinder.rules

@@ -184,7 +184,7 @@ rule fix_bowtie1_log:
     input:
         expand("{sample}/bowtie1/{sample}.log", sample=manager.samples)
     output:
-        "logs/fix_bowtie1_log"
+        "logs/fix_bowtie1_log/done"
     run:
         for filename in input:
             # we read the file
@@ -273,7 +273,7 @@ rule bam_indexing:
 # ========================================================== multiqc
 #
 sequana_multiqc_input = expand("{sample}/bowtie1/{sample}.sorted.bam.bai", sample=sorted(manager.samples))
-sequana_multiqc_input += ["logs/fix_bowtie1_log"]
+sequana_multiqc_input += ["logs/fix_bowtie1_log/done"]
 
 
 rule multiqc: