params.fastq = "$baseDir/data/fastq/*.fastq" log.info "fastq files : ${params.fastq}" log.info "index files : ${params.index}" Channel .fromPath( params.fastq ) .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" } .set { fastq_files } Channel .fromPath( params.index ) .ifEmpty { error "Cannot find any index files matching: ${params.index}" } .set { index_files } process mapping_fastq { tag "$reads.baseName" cpus 4 publishDir "results/mapping/bams/", mode: 'copy' input: file reads from fastq_files file index from index_files.toList() output: file "*.bam" into bam_files file "*_report.txt" into mapping_report script: index_id = index[0] for (index_file in index) { if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) { index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1] } } """ bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \ -q ${reads} 2> \ ${reads.baseName}_bowtie_report.txt | \ samtools view -Sb - > ${reads.baseName}.bam if grep -q "Error" ${reads.baseName}_bowtie_report.txt; then exit 1 fi """ }