diff --git a/src/RNAseq.config b/src/RNAseq.config index 57e50ce54ba1ad8253acdafc2875f8645e4f6cce..339769121c6f51bd561fd0d9a914dd97a6896204 100644 --- a/src/RNAseq.config +++ b/src/RNAseq.config @@ -3,7 +3,7 @@ profiles { process{ withName: trimming { beforeScript = "source $baseDir/.conda_psmn.sh" - conda = "$baseDir/.conda_envs/cutadapt_2.1" + conda = "$baseDir/.conda_envs/cutadapt_2.4" executor = "sge" clusterOptions = "-cwd -V" cpus = 1 diff --git a/src/RNAseq.nf b/src/RNAseq.nf index f153c9324749761193334f651dd85072b9b4f3d6..911314d5c9a98b94e0e12aafa558186e2dcd4ece 100644 --- a/src/RNAseq.nf +++ b/src/RNAseq.nf @@ -27,11 +27,11 @@ process trimming { script: """ cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC \ - -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_tmp_R2.fastq.gz \ - ${reads[0]} ${reads[1]} > ${pair_id}_report.txt + -o ${file_id}_cut_R1.fastq.gz -p ${file_id}_tmp_R2.fastq.gz \ + ${reads[0]} ${reads[1]} > ${file_id}_report.txt - cutadapt -u -14 -o ${pair_id}_cut_R2.fastq.gz ${pair_id}_tmp_R2.fastq.gz \ - > ${pair_id}_cut_report.txt + cutadapt -u -14 -o ${file_id}_cut_R2.fastq.gz ${file_id}_tmp_R2.fastq.gz \ + > ${file_id}_cut_report.txt """ } @@ -82,13 +82,13 @@ log.info "index : ${params.index_hg38}" Channel .fromPath ( params.index_hg38 ) .ifEmpty { error "Cannot find any hg38 index files matching: ${params.index_hg38}" } - .set { index_file_hg38 }--paired + .set { index_file_hg38 } process hisat2_human { tag "$file_id" input: - set file_id, file(fastq_filtred) from rRNA_removed_reads + set file_id, file(fastq_filtred) from rRNA_removed_files file index from index_file_hg38.toList() output: