diff --git "a/src/RNAseq sen1\342\210\206.nf" "b/src/RNAseq sen1\342\210\206.nf" index 8695b03e6fa8717b3462a68f9940f83ceef4c570..eda4e8a0afb8fcb5336f4acc2db0e1ec8adfe754 100644 --- "a/src/RNAseq sen1\342\210\206.nf" +++ "b/src/RNAseq sen1\342\210\206.nf" @@ -10,7 +10,7 @@ * for paired-end data */ -params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq" +params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq.gz" log.info "fastq files : ${params.fastq}" @@ -27,11 +27,11 @@ process adaptor_removal { set pair_id, file(reads) from fastq_files output: - set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut + set pair_id, "*_cut_R{1,2}_001.fastq.gz" into fastq_files_cut script: """ - cutadapt -a TGGAATTCTCGGGTGCCAAGG -g CCTTGGCACCCGAGAATTCCA -A TGGAATTCTCGGGTGCCAAGG -G CCTTGGCACCCGAGAATTCCA \ + cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GTTCAGAGTTCTACAGTCCGACGATC \ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt """