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Preparing Files

You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a header row as shown in the examples below.

Samplesheet input

--input '[path to samplesheet file]'

Samplesheet for QUALITY_ALIGN or AQUASCOPE workflows

Notes:

  • Currently, Illumina, Ion-torrent and Oxford Nanopore platforms are supported in this pipeline.

  • Bedfiles can be a local file path or a raw.github url

The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. It auto-detects sequencing platform (Illumina, Ion-torrent and Oxford nanopore) and determines which set of tools have to be run. The samplesheet must have 7 columns, and have to be in the same order as the header shown below.

A samplesheet file consisting of both single- and paired-end Illumina data may look something like the one below. This is for 2 samples.

sample,platform,fastq_1,fastq_2,lr,bam_file,bedfile
SAMPLE1_PE,illumina,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz,,,https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V3/nCoV-2019.primer.bed
SAMPLE1_SE,illumina,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,,,,https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V3/nCoV-2019.primer.bed
Column Description illumina nanopore iontorrent
sample Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (_). Required Required Required
platform Sequencing platform. This entry will determine the type of sequencing used. It is an important entry as the decision to run a set of tools is determined by this entry. (Accepted entrys: "illumina", "nanopore", "iontorrent") Required Required Required
fastq_1 Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". Required NA NA
fastq_2 Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". Required NA NA
lr Full path to FastQ file for ONT long reads. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". fast5 files are not expected or accepted NA Required NA
bam_file Full path to BAM file for Ion-torrent short reads. File has to .bam strictly NA NA Required
bedfile Full path to local bed file or rawgithub url. File has to .tsv Required Required Required

Samplesheet for FREYJA_ONLY workflow

Option 1. Create a samplesheet using the following reference: 

- [BAM example](../../assets/samplesheet_test_bam.csv)

Option 2. Create samplesheet for primer trimmed bams using the python script bin/bam_to_samplesheet.py 

python bin/bam_to_samplesheet.py \
  --directory <PATH_TO_BAM_FILES> \
  --output <OUTPUT_FILE>"


sample,bam_file
Sample1,test/Sample1.bam
Sample2,test/Sample2.bam
Column Description
sample Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (_).
bam_file Full path to BAM file for Ion-torrent short reads. File has to .bam strictly

Prepare the config files

A. scicomp.config: CDC specific config to run on SciComp resources.

B. test.config is prepared with default parameters; update as needed

Last update: 2025-01-23