Get full URL fromSRA Channel such that I can download fastq files

[Dan_Higgins]

Hi All,
I am new to the community, and I would like to use the fromSRA Channel to download my FASTQ data, but I’m unsure how to obtain the full URL. I can achieve this using the SRA Toolkit, but the fromSRA Channel appears to be a convenient solution if I can get it to work.

I suspect I might be missing something obvious, but I couldn’t find an answer in the documentation.

Any help would be greatly appreciated!!

params.ids =["SRR5851336","SRR5851337","SRR5851338","SRR5851339","SRR5851340","SRR5851341","SRR5851342","SRR5851343","SRR5851344"]
workflow { 
	Channel
    .fromSRA(params.ids,apiKey:'5aXXXXXXXXXXXXXXXXX')
    .view()
}

[SRR5851336, [/vol1/fastq/SRR585/006/SRR5851336/SRR5851336_1.fastq.gz, /vol1/fastq/SRR585/006/SRR5851336/SRR5851336_2.fastq.gz]]
[SRR5851337, [/vol1/fastq/SRR585/007/SRR5851337/SRR5851337_1.fastq.gz, /vol1/fastq/SRR585/007/SRR5851337/SRR5851337_2.fastq.gz]]
[SRR5851338, [/vol1/fastq/SRR585/008/SRR5851338/SRR5851338_1.fastq.gz, /vol1/fastq/SRR585/008/SRR5851338/SRR5851338_2.fastq.gz]]
[SRR5851339, [/vol1/fastq/SRR585/009/SRR5851339/SRR5851339_1.fastq.gz, /vol1/fastq/SRR585/009/SRR5851339/SRR5851339_2.fastq.gz]]
[SRR5851340, [/vol1/fastq/SRR585/000/SRR5851340/SRR5851340_1.fastq.gz, /vol1/fastq/SRR585/000/SRR5851340/SRR5851340_2.fastq.gz]]
[SRR5851341, [/vol1/fastq/SRR585/001/SRR5851341/SRR5851341_1.fastq.gz, /vol1/fastq/SRR585/001/SRR5851341/SRR5851341_2.fastq.gz]]
[SRR5851342, [/vol1/fastq/SRR585/002/SRR5851342/SRR5851342_1.fastq.gz, /vol1/fastq/SRR585/002/SRR5851342/SRR5851342_2.fastq.gz]]
[SRR5851343, [/vol1/fastq/SRR585/003/SRR5851343/SRR5851343_1.fastq.gz, /vol1/fastq/SRR585/003/SRR5851343/SRR5851343_2.fastq.gz]]
[SRR5851344, [/vol1/fastq/SRR585/004/SRR5851344/SRR5851344_1.fastq.gz, /vol1/fastq/SRR585/004/SRR5851344/SRR5851344_2.fastq.gz]]

[mribeirodantas (Marcel Ribeiro-Dantas)]

Hi @Dan_Higgins. Welcome to the community forum

What do you mean by the full URL? As soon as you need it, Nextflow will know where to get the files from. Check the snippet below:

process FASTQC {
    container 'biocontainers/fastqc:v0.11.5'

    input:
    tuple val(sample_id), path(reads_file)

    output:
    path("fastqc_${sample_id}_logs")

    script:
    """
    mkdir fastqc_${sample_id}_logs
    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads_file}
    """
}

workflow {
  params.ids =["SRR5851336","SRR5851337","SRR5851338","SRR5851339","SRR5851340","SRR5851341","SRR5851342","SRR5851343","SRR5851344"]
  Channel
    .fromSRA(params.ids, apiKey: '#my#API#key#here')
    | FASTQC
}

Output (with docker.enabled = true in my nextflow.config file):

[Dan_Higgins]

Hi @mribeirodantas,
Thanks so much.
This works perfectly!
the .vew() was throwing me off by only showing the path and not the URL

I was pretty sure it was something obvious

-Dan