Add functionality to recognise and download SRA/ENA/GEO ids

[drpatelh]

nf-core/viralrecon pull request

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[heuermh]

Might you be able to add a commit with this usage.md doc patch to this pr?

$ git diff .
diff --git a/docs/usage.md b/docs/usage.md
index 79580c3..324c1d4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -235,15 +235,15 @@ AAGGTGTCTGCAATTCATAGCTCT

 ## SRA download

-## `--ignore_sra_errors`
+### `--ignore_sra_errors`

 Ignore validation errors when checking SRA identifiers that would otherwise cause the pipeline to fail (Default: false).

-## `--save_sra_fastq`
+### `--save_sra_fastq`

 Save FastQ files created from SRA identifiers in the results directory (Default: false).

-## `--skip_sra`
+### `--skip_sra`

 Skip steps involving the download and validation of FastQ files using SRA identifiers (Default: false).

[drpatelh]

Done 53b5e86
👍 Good spot.

[JoseEspinosa]

It looks very nice @drpatelh !
The only thing that I would suggest is that if we want to completely get rid of the parallel-fastq-dump process, we could eventually query the US DB when the ftp is not available at the EBI, as we did before ( https://github.com/JoseEspinosa/viralrecon/blob/460a29f962edc31d7818d63b26b6fad5b98d0cbc/bin/check_samplesheet.py#L34-L35 ). One of the fields returned by the query was download_path. We could use this path to download the data using process SRA_FASTQ_FTP. The only problem could be how to retrieve the md5 checksums since this information is not returned by the query and I was trying to find a way to get it from the NCBI but I couldn't find a way yet.

[drpatelh]

Thanks @JoseEspinosa

Querying the NCBI for the fastq files if they dont exist in the ENA doesnt work for this sample 😏

It returns a path to the SRA file I think 🤔 so would still have to be put through parallel-fastq-dump. Think it would be good to keep that process in the pipeline anyway just in case FTP ends up being too slow and if we need to find another way to fetch the files.