bug correction in rule star_to_diffex

RNAja/snakefiles/Snakefile

@@ -267,7 +267,7 @@ rule star_map_count:
         other = config['PARAMS']['STAR']['mapping']["params"],
         R2= f"{fastq_dir}/{{fastq}}_R2{RNAja_obj.fastq_files_ext}" if config['DATA']['PAIRED'] else '',
     output:
-        bam = f"{output_dir}/COUNT/STAR/{{fastq}}Aligned.out.sam",
+        bam = f"{output_dir}/COUNT/STAR/{{fastq}}Aligned.out.bam",
         genecount= f"{output_dir}/COUNT/STAR/{{fastq}}ReadsPerGene.out.tab",
         bam_sort= f"{output_dir}/MAPPING/STAR/{{fastq}}.bam",
     log :
@@ -333,10 +333,10 @@ rule star_to_diffex:
         """
         (
         # retrieve the 4th column of each "ReadsPerGene.out.tab" file + the first column that contains the gene IDs
-        paste {input.countsfiles} | grep -v "_" | awk '{{printf "%s\t", $1}}{{for (i=4;i<=NF;i+=4) printf "%s\t", $i; printf "\n" }}' > {output.intermediate_result}
+        paste {input.countsfiles} | grep -v '_' | awk '{{printf "%s\\t", $1}}{{for (i=4;i<=NF;i+=4) printf "%s\\t", $i; printf "\\n" }}' > {output.intermediate_result}
         
         # add header: "gene_name" + the name of each of the counts file
-        sed -e "1igene_name\t$(ls {input.countsfiles} | tr '\n' '\t' | sed 's/ReadsPerGene.out.tab//g')" tmp | cut -f1-7 > {output.stargenecount}
+        sed -e "1igene_name\\t$(ls {input.countsfiles} | tr '\\n' '\\t' | sed 's/ReadsPerGene.out.tab//g')" {output.intermediate_result} | cut -f1-7 > {output.stargenecount}
         ) 1>{log.output} 2>{log.error}
         """