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¶
- Create a samplesheet using the following reference:
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 |
|---|---|
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 (_). |
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. |
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". |
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". |
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 |
bam_file | Full path to BAM file for Ion-torrent short reads. File has to .bam strictly |
bedfile | Full path to local bed file or rawgithub url. File has to .tsv |
Samplesheet for FREYJA_ONLY workflow¶
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 |
Option 1. Create a samplesheet using the following reference: - BAM example
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>"
Prepare the config files¶
Prepare the configuration files
A. scicomp.config: CDC specific config to run on SciComp resources.
B. test.config is prepared with default parameters; update as needed