diff --git a/src/nf_modules/minimap2/main.nf b/src/nf_modules/minimap2/main.nf index 5ac898204bd348dde6582630908d0e528721d1f5..9dbe5a575f840d9b911f778b7adf039747a6024f 100644 --- a/src/nf_modules/minimap2/main.nf +++ b/src/nf_modules/minimap2/main.nf @@ -16,7 +16,6 @@ process index_fasta { output: tuple val(file_id), path("${fasta}"), path("*.mmi*"), emit: index - path "*_report.txt", emit: report script: memory = "${task.memory}" - ~/\s*GB/ @@ -41,7 +40,6 @@ process mapping_fastq { output: tuple val(file_id), path("*.bam"), emit: bam - path "*_report.txt", emit: report script: if (file_id instanceof List){ @@ -50,7 +48,7 @@ process mapping_fastq { file_prefix = file_id } memory = "${task.memory}" - ~/\s*GB/ - memory = memory / (task.cpus + 1.0) + memory = memory.toInteger() / (task.cpus + 1.0) if (reads.size() == 2) """ minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} | @@ -61,4 +59,4 @@ process mapping_fastq { minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads} | samtools view -Sb - > ${pair_id}.bam """ -} \ No newline at end of file +}