subsampler_only - WDL Atlas

WORKFLOW subsampler_only

File Path	`pipes/WDL/workflows/subsample_by_casecounts.wdl`
WDL Version	1.0
Type	workflow

Imports

Namespace	Path
`interhost`	`../tasks/tasks_interhost.wdl`

Workflow: subsampler_only

Inputs

Name	Type	Description	Default
`metadata`	`File`	-	-
`case_data`	`File`	-	-
`id_column`	`String`	-	-
`geo_column`	`String`	-	-
`keep_file`	`File?`	-	-
`remove_file`	`File?`	-	-
`filter_file`	`File?`	-	-
`seed_num`	`Int?`	-	-
`start_date`	`String?`	-	-
`end_date`	`String?`	-	-
5 optional inputs with default values
`date_column`	`String`	-	"date"
`unit`	`String`	-	"week"
`baseline`	`Float`	-	0.0001
`docker`	`String`	-	"quay.io/broadinstitute/subsampler"
`machine_mem_gb`	`Int`	-	30

Outputs

Name	Type	Expression
`genome_matrix_days_file`	`File`	`subsample_by_cases.genome_matrix_days`
`matrix_genomes_unit_file`	`File`	`subsample_by_cases.matrix_genomes_unit`
`matrix_cases_unit_file`	`File`	`subsample_by_cases.matrix_cases_unit`
`weekly_sampling_proportions_file`	`File`	`subsample_by_cases.weekly_sampling_proportions`
`weekly_sampling_bias_file`	`File`	`subsample_by_cases.weekly_sampling_bias`
`matrix_genomes_unit_corrected_file`	`File`	`subsample_by_cases.matrix_genomes_unit_corrected`
`selected_sequences_file`	`File`	`subsample_by_cases.selected_sequences`
`selected_metadata_file`	`File`	`subsample_by_cases.selected_metadata`
`sampling_stats_file`	`File`	`subsample_by_cases.sampling_stats`

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `subsample_by_cases` ↗

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

subsample_by_cases

← Back to Index

flowchart TD
    Start([subsampler_only])
    N1["subsample_by_cases"]
    Start --> N1
    N1 --> End([End])
    classDef taskNode fill:#a371f7,stroke:#8b5cf6,stroke-width:2px,color:#fff
    classDef workflowNode fill:#58a6ff,stroke:#1f6feb,stroke-width:2px,color:#fff

version 1.0

import "../tasks/tasks_interhost.wdl" as interhost

workflow subsampler_only {

    call interhost.subsample_by_cases

    output {
        File    genome_matrix_days_file             =   subsample_by_cases.genome_matrix_days
        File    matrix_genomes_unit_file            =   subsample_by_cases.matrix_genomes_unit
        File    matrix_cases_unit_file              =   subsample_by_cases.matrix_cases_unit
        File    weekly_sampling_proportions_file    =   subsample_by_cases.weekly_sampling_proportions
		File    weekly_sampling_bias_file           =   subsample_by_cases.weekly_sampling_bias
		File    matrix_genomes_unit_corrected_file  =   subsample_by_cases.matrix_genomes_unit_corrected
        File    selected_sequences_file             =   subsample_by_cases.selected_sequences
        File    selected_metadata_file              =   subsample_by_cases.selected_metadata
        File    sampling_stats_file                 =   subsample_by_cases.sampling_stats
    }
}