fixe issues with names of variables

workflow/rules/star_index.rules

@@ -43,22 +43,25 @@ rule star_index:
     shell:
         """
         set +o pipefail
-        GenomeLength=`grep -v ">" {input.fasta} | tr -d '\n' | wc -c`
+        tmp="{input}"
+        infiles=($tmp)
+
+        GenomeLength=`grep -v ">" ${{infiles[0]}} | tr -d '\n' | wc -c`
         SAindex=$(echo $GenomeLength | awk '{{a=log($1)/2 - 1; if (a>14) a=14; printf("%d\\n",a)}}')
-        NumberOfReferences=`grep -c ">" {input.fasta}`
+        NumberOfReferences=`grep -c ">" ${{infiles[0]}}`
         ChrBin=$(echo | awk -v g=$GenomeLength -v n=$NumberOfReferences '{{a=log(g/n); if (a>18) a=18; printf("%d\\n",a)}}' )
 
-        if [[ -s {input.gff_file} && {input.gff_file} == "*.gtf"  ]]
+        if [[ -s ${{infiles[1]}} && ${{infiles[1]}} == "*.gtf"  ]]
         then
-            STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile {input.gff_file} --genomeSAindexNbases $SAindex --genomeChrBinNbits $ChrBin
-        elif [[ -s {input.gff_file} && {input.gff_file} == "*.gff" ]]
+            STAR --runMode genomeGenerate --genomeFastaFiles ${{infiles[0]}} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile ${{infiles[1]}} --genomeSAindexNbases $SAindex --genomeChrBinNbits $ChrBin
+        elif [[ -s ${{infiles[1]}} && ${{infiles[1]}} == "*.gff" ]]
         then
-             STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile {input.gff_file} --sjdbGTFtagExonParentTranscript Parent --genomeSAindexNbases $SAindex --genomeChrBinNbits $ChrBin
+             STAR --runMode genomeGenerate --genomeFastaFiles ${{infiles[0]}} --genomeDir {params.wkdir} --runThreadN {threads} --sjdbGTFfile ${{infiles[1]}} --sjdbGTFtagExonParentTranscript Parent --genomeSAindexNbases $SAindex --genomeChrBinNbits $ChrBin
         else
-            STAR --runMode genomeGenerate --genomeFastaFiles {input.fasta} --genomeDir {params.wkdir} --runThreadN {threads} --genomeSAindexNbases $SAindex --genomeChrBinNbits $ChrBin
+            STAR --runMode genomeGenerate --genomeFastaFiles ${{infiles[0]}} --genomeDir {params.wkdir} --runThreadN {threads} --genomeSAindexNbases $SAindex --genomeChrBinNbits $ChrBin
         fi
         
-        samtools faidx {input.fasta}
+        samtools faidx ${{infiles[0]}}
 
         """