2. Preparing Files
Prepare the Samplesheet¶
Prepare the assets/samplesheet.csv
A. Create additional sample sheets using the following samplesheet as reference.
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 |
B. Currently, Illumina, Ion-torrent and Oxford Nanopore platforms are supported in this pipeline.
D. Keywords: lr - Longreads, bam_file - Only for Ion-torrent platform, platform - sequencing platform.
Prepare the config files¶
Prepare the configuration files
A. cdc-dev.config: All CDC-users must use the cdc-dev.config to run the pipeline on Rosalind cluster.
B. test.config is prepared with default parameters, update as needed
Last update: 2024-05-16