Fix bowtie1 regression (log).

enforce usage of --genome-directory (set to None)

README.rst

@@ -158,6 +158,8 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.19.2    * fix bowtie1 regression in the log file
+          * set genome directory default to None to enforce its usage
 0.19.1    * add rnaseqc container.
           * Update rseqc rules (redirection)
           * cleanup onsuccess rule

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-rnaseq"
-version = "0.19.1"
+version = "0.19.2"
 description = "A RNAseq pipeline from raw reads to feature counts"
 authors = ["Sequana Team"]
 license = "BSD-3"

sequana_pipelines/rnaseq/main.py

@@ -60,7 +60,6 @@
 @click.option(
     "--genome-directory",
     "genome_directory",
-    default=".",
     show_default=True,
     type=click.Path(dir_okay=True, file_okay=False),
     required=True,

sequana_pipelines/rnaseq/rnaseq.rules

@@ -484,7 +484,7 @@ if manager.config.general.rRNA_feature or manager.config.general.contaminant_fil
         input:
             expand("{sample}/bowtie1_mapping_rna/{sample}_bowtie1.log", sample=manager.samples)
         output:
-            "logs/fix_bowtie1_log"
+            "logs/fix_bowtie1/{sample}.log"
         run:
 
             for filename in input:
@@ -501,7 +501,7 @@ if manager.config.general.rRNA_feature or manager.config.general.contaminant_fil
                             fout.write(line)
             with open(output[0], "w") as fout:
                 fout.write("")
-    expected_output += ["logs/fix_bowtie1_log"]
+    expected_output += expand("logs/fix_bowtie1/{sample}.log", sample=manager.samples)
 
 
 # ========================================================== bowtie2 mapping