diff --git "a/src/RNAseq sen1\342\210\206.nf" "b/src/RNAseq sen1\342\210\206.nf" new file mode 100644 index 0000000000000000000000000000000000000000..8695b03e6fa8717b3462a68f9940f83ceef4c570 --- /dev/null +++ "b/src/RNAseq sen1\342\210\206.nf" @@ -0,0 +1,38 @@ +/* +* cutadapt : +* Imputs : fastq files +* Output : fastq files +*/ + +/* Small RNA-seq Illumina adaptor removal NEXTflex Small RNA Seq Kit v3 */ + +/* +* for paired-end data +*/ + +params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq" + +log.info "fastq files : ${params.fastq}" + +Channel + .fromFilePairs( params.fastq ) + .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" } + .set { fastq_files } + +process adaptor_removal { + tag "$pair_id" + publishDir "results/fastq/adaptor_removal/", mode: 'copy' + + input: + set pair_id, file(reads) from fastq_files + + output: + set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut + + script: + """ + cutadapt -a TGGAATTCTCGGGTGCCAAGG -g CCTTGGCACCCGAGAATTCCA -A TGGAATTCTCGGGTGCCAAGG -G CCTTGGCACCCGAGAATTCCA \ + -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \ + ${reads[0]} ${reads[1]} > ${pair_id}_report.txt + """ +}