diff --git a/src/RNAseq.nf b/src/RNAseq.nf index d26d66807602c7565433e1c1dba47f3c7c73da18..2e9224244968c16be327bb0d7ceb92f50aa836e9 100644 --- a/src/RNAseq.nf +++ b/src/RNAseq.nf @@ -128,7 +128,7 @@ process index_fasta { publishDir "results/mapping/index/", mode: 'copy' input: - file fasta from fasta_files + file fasta from fasta_files_extracted output: file "*.index*" into index_files @@ -152,8 +152,8 @@ process mapping_fastq { publishDir "results/mapping/quantification/", mode: 'copy' input: - file reads from fastq_files - file index from index_files.toList() + file reads from fastq_files_trim + file index from index_files output: file "*" into counts_files @@ -168,31 +168,5 @@ ${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt } -/* -* for single-end data -*/ - - -process mapping_fastq { - tag "$reads.baseName" - cpus 4 - publishDir "results/mapping/quantification/", mode: 'copy' - - input: - file reads from fastq_files_trim - file index from index_files - - output: - file "*" into count_files - - script: -""" -mkdir ${reads.baseName} -kallisto quant -i ${index} -t ${task.cpus} --single ---bias --bootstrap-samples 100 -o ${reads.baseName} \ --l ${params.mean} -s ${params.sd} -o ./ \ -${reads} > ${reads.baseName}_kallisto_report.txt -""" -}