correct bugs:

- fastq.gz should be uncompressed for star
- changer genomedir for star mapping

RNAja/install_files/config.yaml

@@ -15,5 +15,7 @@ PARAMS:
     STAR:
         indexation:
             params: "--sjdbOverhang 100 --genomeSAindexNbases 10"
+        mapping:
+            params: "--readFilesCommand zcat"
     STRINGTIE:
         discovery_mode : true

RNAja/install_files/config_test/RNAja-config_paired.yaml

@@ -16,6 +16,6 @@ PARAMS:
         indexation:
             params: "--sjdbOverhang 100 --genomeSAindexNbases 10"
         mapping:
-            params: ""
+            params: "--readFilesCommand zcat"
     STRINGTIE:
         discovery_mode : true

RNAja/install_files/config_test/RNAja-config_single.yaml

@@ -16,6 +16,6 @@ PARAMS:
         indexation:
             params: "--sjdbOverhang 100 --genomeSAindexNbases 10"
         mapping:
-            params: ""
+            params: "--readFilesCommand zcat"
     STRINGTIE:
         discovery_mode : true

RNAja/snakefiles/Snakefile

@@ -224,7 +224,7 @@ rule star_index:
         other=config['PARAMS']['STAR']['indexation']["params"]
     output:
         ref_link=f"{output_dir}/REF/STAR/{reference_basename}.fasta",
-        index=f"{output_dir}/REF/STAR/{reference_basename}.fasta.1.ht2",
+        index=f"{output_dir}/REF/STAR/genomeParameters.txt",
     message:
         """                                                                                                                                                                                   
         Execute {rule}                                                                                                                                                            
@@ -281,7 +281,7 @@ rule star_map:
     shell :
         """
         (
-        STAR --genomeDir {output_dir}/2_MAPPING/STAR/ \
+        STAR --genomeDir {output_dir}/REF/STAR/ \
         --runThreadN {threads} \
         --readFilesIn {input.R1} {params.R2} \
         {params.other} \