filter_sequences - WDL Atlas

WORKFLOW filter_sequences

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

Imports

Namespace	Path
`nextstrain`	`../tasks/tasks_nextstrain.wdl`

Workflow: filter_sequences

Filter and subsample a sequence set. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/filter.html

Inputs

Name	Type	Description	Default
`sequences_fasta`	`File`	-	-
`sample_metadata_tsv`	`File`	-	-
`sequences_per_group`	`Int?`	-	-
`group_by`	`String?`	-	-
`include`	`File?`	-	-
`exclude`	`File?`	-	-
`min_date`	`Float?`	-	-
`max_date`	`Float?`	-	-
`min_length`	`Int?`	-	-
`priority`	`File?`	-	-
`subsample_seed`	`Int?`	-	-
`exclude_where`	`Array[String]?`	-	-
`include_where`	`Array[String]?`	-	-
3 optional inputs with default values
`non_nucleotide`	`Boolean`	-	true
`docker`	`String`	-	"docker.io/nextstrain/base:build-20240318T173028Z"
`disk_size`	`Int`	-	750

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS `filter` ↗ → filter_subsample_sequences

No explicit input mappings

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image

⚙️ Parameterized

Configured via input:
docker

Used by 1 task:

filter

← Back to Index

flowchart TD
    Start([filter_sequences])
    N1["filter
filter_subsample_sequences"]
    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_nextstrain.wdl" as nextstrain

workflow filter_sequences {
    meta {
        description: "Filter and subsample a sequence set. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/filter.html"
    }

    call nextstrain.filter_subsample_sequences as filter
}