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Commit ce834706 authored by elabaron's avatar elabaron
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fix beug

parent cfa378ed
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...@@ -98,7 +98,7 @@ process hisat2 { ...@@ -98,7 +98,7 @@ process hisat2 {
""" """
hisat2 -x ${index_id} -p ${task.cpus} \ hisat2 -x ${index_id} -p ${task.cpus} \
-1 ${fastq_filtred[0]} -2 ${fastq_filtred[1]} --un-conc-gz ${file_id}_notaligned_hisat_R%.fastq.gz \ -1 ${fastq_filtred[0]} -2 ${fastq_filtred[1]} --un-conc-gz ${file_id}_notaligned_hisat_R%.fastq.gz \
--rna-strandness 'F' --dta --no-temp-splicesite \ --rna-strandness 'F' \
2> ${file_id}_hisat2_NY5.txt | samtools view -F 4 -F 16 -Sb - > ${file_id}.bam 2> ${file_id}_hisat2_NY5.txt | samtools view -F 4 -F 16 -Sb - > ${file_id}.bam
if grep -q "ERR" ${file_id}_hisat2_NY5.txt ; then if grep -q "ERR" ${file_id}_hisat2_NY5.txt ; then
...@@ -169,7 +169,7 @@ process merge_bam{ ...@@ -169,7 +169,7 @@ process merge_bam{
for i in *.txt ; do for i in *.txt ; do
echo \$i echo \$i
cat \$i > \${i::-4}_new.txt cat \$i >> \${i::-4}_new.txt
done done
""" """
......
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