Introduction

DOH-JDJ0303/bs-fetch-nf is a bioinformatics pipeline that:

1. downloads reads from Illumina BaseSpace using a supplied list of Illumina biosample names, dataset names, or FASTQ file IDs and saves them in a subdirectory called 'reads/'.
2. creates a manifest file containing information about the newly downloaded reads in a desired format.

Usage

Step 1. Clone the repository

git clone https://github.com/DOH-JDJ0303/bs-fetch-nf

Step 2. Prepare the input file and save as a .csv

Prepare a file containg a list of Illumina biosample names, dataset names, or file IDs. Each name or ID should be listed on a new line (see example below).

isolate1
isolate2
isolate3
isolate4

Step 3. Run the pipeline

From your local repository run the pipeline using the general command structure below:

nextflow run main.nf \
    -profile docker \
    --input samples.csv \
    --output 's3://my-bucket/mycosnp/run1/' \
    --run_name 'test_fetch'
    --access_token '312g4hjgj12hjj1hg43hj12gj3h' \
    --input_format 'biosample' \
    --output_format 'generic'

Argument Descriptions

Required

--input file containing biosamples names, dataset names, or file IDs. must be .csv
--output absolute path to where the outputs should be saved
--run_name your designated run name (output directory will be created with this name) --access_token your Illumina BaseSpace access token

Optional

--input_format the input format (i.e., 'biosample', 'dataset', 'file_id'; default: 'biosample')
--output_format the format of the manifest file (i.e., 'generic', 'mycosnp', 'phoenix'; default: 'generic')
--api_server your Illumina BaseSpace API server path (default: 'https://api.basespace.illumina.com')

Pipeline output

This pipeline generates two main outputs:

1. The reads downloaded from BaseSpace. These are saved in a subdirectory of the specified output directory called reads/.
2. A manifest file in the specified format saved in the specified output directory. \

Note: There is currently only one manifest format supported (see example below). This format can be used for the CDC MycoSNP and PHoeNIx pipelines. \

Output Format 1: 'generic', 'mycosnp', and 'phoenix'

sample,fastq_1,fastq_2
isolate1,s3://my-bucket/mycosnp/run1/reads/isolate1_R1_001.fastq.gz,s3://my-bucket/mycosnp/run1/reads/isolate1_R2_001.fastq.gz
isolate2,s3://my-bucket/mycosnp/run1/reads/isolate2_R1_001.fastq.gz,s3://my-bucket/mycosnp/run1/reads/isolate2_R2_001.fastq.gz
isolate3,s3://my-bucket/mycosnp/run1/reads/isolate3_R1_001.fastq.gz,s3://my-bucket/mycosnp/run1/reads/isolate3_R2_001.fastq.gz
isolate4,s3://my-bucket/mycosnp/run1/reads/isolate4_R1_001.fastq.gz,s3://my-bucket/mycosnp/run1/reads/isolate4_R2_001.fastq.gz

Credits

nf-core/bsfetch was originally written by Jared Johnson

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.