get good log output for multiQC

workflow/rules/sortmerna.rules

@@ -29,7 +29,7 @@ rule sortmerna:
         fasta = sortmerna_fasta
     output:
         rRNA = temp(sortmerna_outfile_rRNA),
-        no_rRNA = sortmerna_outfile_no_rRNA
+        no_rRNA = temp(sortmerna_outfile_no_rRNA)
     params:
          tmpdir = config['tmpdir']
     singularity:
@@ -54,7 +54,6 @@ rule sortmerna:
         tmp="{output.no_rRNA}"
         outnorRNA=($tmp)
  
- 
         fasta="{input.fasta}"
         idxdir=$(dirname ${{fasta}})"/sortmerna/"
         
@@ -66,6 +65,8 @@ rule sortmerna:
             ext=""
         fi
 
+        if [ -d {params.tmpdir}/{wildcards.SAMPLE} ]; then rm -rf {params.tmpdir}/{wildcards.SAMPLE} ; fi
+
         if [[ ${{#infiles[@]}} -eq 2 ]];
         then
             sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir}/{wildcards.SAMPLE} -threads {threads} --reads ${{infiles[0]}} --reads ${{infiles[1]}} --aligned out_paired_ribo --fastx --out2 --paired_out --other out_paired  -v > {log.out} 2> {log.err}
@@ -73,14 +74,17 @@ rule sortmerna:
             mv out_paired_rev.fq${{ext}} {{outnorRNA[1]}}
             mv out_paired_ribo_fwd.fq${{ext}} {{outrRNA[0]}}
             mv out_paired_ribo_rev.fq${{ext}} {{outrRNA[1]}}
+            mv output.rRNA.log {log.out}
 
         else
             sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir}/{wildcards.SAMPLE} -threads {threads} --reads {input.fastq} --aligned output.rRNA --fastx --other output.no_rRNA  -v  > {log.out} 2> {log.err}
             mv output.no_rRNA.fq${{ext}} {output.no_rRNA}
             mv output.rRNA.fq${{ext}} {output.rRNA}
+            mv output.rRNA.log {log.out}
         fi
 
 
         rm -rf {params.tmpdir}/{wildcards.SAMPLE}
 
         """
+