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Commit ba8ad15c authored by elabaron's avatar elabaron
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src/RNAseq.nf : correct hisat mapping

parent 76474bcf
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......@@ -229,8 +229,9 @@ hisat2 -x ${index_id} \
-1 ${fastq_filtred[0]} \
-2 ${fastq_filtred[1]} \
--un-conc-gz ${file_id}_notaligned_R%.fastq.gz \
--rna-strandness 'F' \
2> ${file_id}.txt \
--rna-strandness 'FR' \
--dta \
2> ${file_id}_genome.txt \
| samtools view -bS -F 4 - \
| samtools sort -@ ${task.cpus} -o ${file_id}.bam \
&& samtools index ${file_id}.bam
......@@ -245,7 +246,7 @@ HISAT_ALIGNED.into{HISAT_ALIGNED_FASTQC;
HISAT_ALIGNED_DEDUP}
/* Fastqc of filtred reads */
/* Fastqc of genome reads */
process fastqc_genome {
tag "$file_id"
......@@ -401,7 +402,8 @@ hisat2 -x ${index2_id} \
-p ${task.cpus} \
-1 ${fastq_unaligned[0]} \
-2 ${fastq_unaligned[1]} \
--rna-strandness 'F' \
--rna-strandness 'FR' \
--dta\
2> ${file_id}_postgenome.txt \
| samtools view -bS -F 4 - \
| samtools sort -@ ${task.cpus} -o ${file_id}.bam \
......
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