From d77dede7092bacf5a4aafbeb8829ba46cf8e1566 Mon Sep 17 00:00:00 2001
From: Rachel LEGENDRE <rachel.legendre@pasteur.fr>
Date: Wed, 15 Mar 2023 13:38:43 +0100
Subject: [PATCH] fixe issues with names of variables
---
workflow/rules/star_index.rules | 19 +++++++++++--------
1 file changed, 11 insertions(+), 8 deletions(-)
diff --git a/workflow/rules/star_index.rules b/workflow/rules/star_index.rules
index b14843f..6dacca4 100755
--- a/workflow/rules/star_index.rules
+++ b/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]}}
"""
--
GitLab