debug raw_gff3

tools/hisat2_index/hisat2_index.rule.snakefile

@@ -11,7 +11,7 @@ rule <step_name>__hisat2_index:
         config["<step_name>__hisat2_index_threads"]
     params:
         command = config["<step_name>__hisat2_index_command"],
-        output_prefix = config["<step_name>__hisat2_index_output_dir"]+"/index"
+        output_prefix = config["results_dir"]+"/"+config["<step_name>__hisat2_index_output_dir"]+"/index"
     shell:
         "{params.command} "
         "{input.genome_fasta} "

tools/htseq_count/htseq_count.rule.snakefile

@@ -9,6 +9,7 @@ rule <step_name>__htseq_count:
         command = config["<step_name>__htseq_count_command"],
         htseq_count_minaqual = config["<step_name>__htseq_count_minaqual"],
         htseq_stranded = config["<step_name>__htseq_stranded"],
+        htseq_orientation = config["<step_name>__htseq_orientation"],
         output_dir = config["results_dir"]+'/'+config["<step_name>__htseq_count_output_dir"]
     shell:
         "{params.command} -f bam -a  {params.htseq_count_minaqual}  -s {params.htseq_stranded} -r {params.htseq_orientation} {input.bam} {input.gff_file} 2> {log} > {output.stats}"