4.39. fetch_sra_to_bam¶

Retrieve reads from the NCBI Short Read Archive in unaligned BAM format with relevant metadata encoded.

4.39.1. Inputs¶

fetch_sra_to_bam.Fetch_SRA_to_BAM.SRA_ID
String — Default: None
???

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fetch_sra_to_bam.check_terra_env.docker
String — Default: "quay.io/broadinstitute/viral-core:2.5.21"
???

fetch_sra_to_bam.email_address
String? — Default: None
???

fetch_sra_to_bam.Fetch_SRA_to_BAM.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.11.1"
???

fetch_sra_to_bam.Fetch_SRA_to_BAM.machine_mem_gb
Int? — Default: None
???

fetch_sra_to_bam.Fetch_SRA_to_BAM.ncbi_api_key
String? — Default: None
???

fetch_sra_to_bam.Fetch_SRA_to_BAM.sample_name
String? — Default: None
???

fetch_sra_to_bam.biosample_accession
String
???

fetch_sra_to_bam.library_id
String
???

fetch_sra_to_bam.reads_ubam
File
???

fetch_sra_to_bam.run_date
String
???

fetch_sra_to_bam.sample_collected_by
String
???

fetch_sra_to_bam.sample_collection_date
String
???

fetch_sra_to_bam.sample_geo_loc
String
???

fetch_sra_to_bam.sample_strain
String
???

fetch_sra_to_bam.sequencing_center
String
???

fetch_sra_to_bam.sequencing_platform
String
???

fetch_sra_to_bam.sequencing_platform_model
String
???

fetch_sra_to_bam.sra_metadata
File
???

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