genbank_dump
pipes/WDL/workflows/sarscov2_genbank_ingest.wdl

WORKFLOW genbank_dump

File Path pipes/WDL/workflows/sarscov2_genbank_ingest.wdl
WDL Version 1.0
Type mixed

📋Tasks in this document

Workflow: genbank_dump

Inputs

Name Type Description Default
Google_Maps_API_Key_File File - -
user_email String - -

Outputs

Name Type Expression
seqs_fasta File pull_data.genbank_seqs_fasta
seqs_metadata File pull_data.genbank_seqs_metadata

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS pull_data

Input Mappings (2)
Input Value
Google_Maps_API_Key_File Google_Maps_API_Key_File
user_email user_email

Images

Container images used by tasks in this workflow:

🐳 pathogen-genomics

cmloreth/pathogen-genomics:test

Used by 1 task:
  • pull_data

Tasks

TASKS pull_data

Inputs

Name Type Description Default
Google_Maps_API_Key_File File - -
user_email String - -

Command

python3 ~/scripts/genbank_dump.py -k ~{Google_Maps_API_Key_File} -e ~{user_email}

Outputs

Name Type Expression
genbank_seqs_fasta File 'genbank_seqs.fasta'
genbank_seqs_metadata File 'genbank_seq_metadata.tsv'

Runtime

Key Value
docker "cmloreth/pathogen-genomics:test"
memory "1 GB"
cpu 1
disks "local-disk 100 HDD"
dx_instance_type "mem1_ssd1_v2_x2"
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genbank_dump - Workflow Graph

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genbank_dump - WDL Source Code

version 1.0

workflow genbank_dump {
    input {
        File  Google_Maps_API_Key_File
        String  user_email
    }
    call pull_data {
        input:
            Google_Maps_API_Key_File = Google_Maps_API_Key_File,
            user_email               = user_email
    }
    output {
        File seqs_fasta    = pull_data.genbank_seqs_fasta
        File seqs_metadata = pull_data.genbank_seqs_metadata
    }
}


task pull_data {

    input {
        File  Google_Maps_API_Key_File
        String  user_email
    }

    command {
        python3 ~/scripts/genbank_dump.py -k ~{Google_Maps_API_Key_File} -e ~{user_email}
    }

    output {
      File genbank_seqs_fasta    = 'genbank_seqs.fasta'
      File genbank_seqs_metadata = 'genbank_seq_metadata.tsv'
    }

    runtime {
      docker: "cmloreth/pathogen-genomics:test"
      memory: "1 GB"
      cpu: 1
      disks: "local-disk 100 HDD"
      dx_instance_type: "mem1_ssd1_v2_x2"
    }
}