Running NextFlow using AWS Batch

Processing Genomics workflows require a variety of tools with distinct computing resources requirements. Some of these requirements are merely beyond the configuration of powerful workstations. High-performance clusters (HPC) offer the possibility to scale up computing resources to meet the increasing demands of these processes. However, maintaining the infrastructure of an on-premises HPC may not be a viable solution for many parities. A more cost-effective method is to provide computer resources dynamically by leveraging cloud computing....

May 1, 2021 · 6 min · Firas Sadiyah

Using RegEx to capture file name in Groovy/NextFlow

My sequencing files are named according to the folowing pattern lane5651_AAGAGGCA_00h_Cell_WT3_L008_R1.fastq.gz. I would like to capture the Sample ID as 00h_Cell_WT3 in order to name all downstream files accordingly. To this end, I wrote the following snippet: 1#!/usr/bin/env nextflow 2 3// fastq files are stored in reads as paired ends R1 and R4 4params.reads = 'reads/lane*_*_*_*_R{1,4}.fastq.gz' 5 6Channel 7 .fromFilePairs(params.reads, flat: true) 8 .map { prefix, file1, file2 -> tuple(getSampleID(prefix), file1, file2) } 9 ....

October 6, 2018 · 2 min · Firas Sadiyah