adapt sortmerna rule to new version

workflow/rules/sortmerna.rules

@@ -30,6 +30,8 @@ rule sortmerna:
     output:
         rRNA = temp(sortmerna_outfile_rRNA),
         no_rRNA = temp(sortmerna_outfile_no_rRNA)
+    params:
+         tmpdir = config['tmpdir']
     singularity:
         "rnaflow.img"
     shadow: "shallow"
@@ -38,25 +40,28 @@ rule sortmerna:
         out = sortmerna_logs_out
     threads: 6
     envmodules:
-        "sortmerna/2.1b"
+        "sortmerna/4.3.4"
     shell:
         """
         set +o pipefail
-        #tmp="{input.fastq}"
-        #infiles=($tmp)
+        tmp="{input.fastq}"
+        infiles=($tmp)
         fasta="{input.fasta}"
-        index=${{fasta%.fa}}
+        idxdir=$(dirname ${{fasta}})"/sortmerna/"
 
-        if [[ ! -s ${{index}}.stats ]]
-        then
-            indexdb_rna --ref ${{fasta}},${{index}}
-        fi
 
+        if [[ ${{#infiles[@]}} -eq 2 ]];
+        then
+            sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir} -threads {threads} --reads ${{infiles[0]}} --reads ${{infiles[1]}} --aligned {output.rRNA} --fastx --out2 --paired_out --other {output.no_rRNA}  -v > {log.out} 2> {log.err}
+            mv {output.no_rRNA}.fastq {output.no_rRNA}
+            mv {output.rRNA}.fastq {output.rRNA}
 
-        sortmerna --ref ${{fasta}},${{index}} -a {threads} --reads {input.fastq} --aligned {output.rRNA} --fastx --other {output.no_rRNA} --log -v > {log.out} 2> {log.err}
+        else
+            sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir} -threads {threads} --reads ${{infiles[0]}} --aligned {output.rRNA} --fastx --other {output.no_rRNA}  -v > {log.out} 2> {log.err}
+            mv {output.no_rRNA}.fastq {output.no_rRNA}
+            mv {output.rRNA}.fastq {output.rRNA}
+        fi
 
 
-        mv {output.no_rRNA}.fastq {output.no_rRNA}
-        mv {output.rRNA}.fastq {output.rRNA}
 
         """