Overview
Install NextFlow locally
PBS session: qsub -I -S /bin/bash -l walltime=168:00:00 -l select=1:ncpus=4:mem=8gb
tmux
module load java
Test NextFlow: nextflow run nf-core/ampliseq -profile test,singularity --metadata "Metadata.tsv"
failed! Data files listed in metadata.tsv not found. Need local copies for this parameter.
Tried without metadata: NextFlow: nextflow run nf-core/ampliseq -profile test,singularity
Initially ran, then failed during trimming '
cutadapt: error: pigz: abort: read error on 1_S103_L001_R2_001.fastq.gz (No such file or directory) (exit code 2)' Looks like cannot pull down files. Need to pull files locally.s
6. Run Nextflow tower
7.
Pipeline overview
This section provides a skeleton overview of the pipeline commands. if you’ve run this pipeline before and understand the following sections, you can simply run these commands on your data. if this is your first time running this analysis, it’s strongly recommended you read the following sections of this article, as they provide important background information.