amplicon16S_analysis
pipes/WDL/workflows/classify_qiime2_multi.wdl

WORKFLOW amplicon16S_analysis

File Path pipes/WDL/workflows/classify_qiime2_multi.wdl
WDL Version 1.0
Type workflow

Imports

Namespace Path
qiime ../tasks/tasks_16S_amplicon.wdl

Workflow: amplicon16S_analysis

Running 16S amplicon (from BAM format) sequencing analysis with qiime.

Author: fnegrete
viral_ngs@broadinstitute.org

Inputs

Name Type Description Default
reads_bam Array[File] - -
trained_classifier File - -
keep_untrimmed_reads Boolean - -
24 optional inputs with default values

Calls

This workflow calls the following tasks or subworkflows:

CALL TASKS qiime_import_from_bam ↗

Input Mappings (1)
Input Value
reads_bam reads_bam

CALL TASKS trim_reads ↗

Input Mappings (2)
Input Value
reads_qza qiime_import_from_bam.reads_qza
keep_untrimmed_reads keep_untrimmed_reads

CALL TASKS join_paired_ends ↗

Input Mappings (1)
Input Value
trimmed_reads_qza trim_reads.trimmed_reads_qza

CALL TASKS deblur ↗

Input Mappings (1)
Input Value
joined_end_reads_qza join_paired_ends.joined_end_reads_qza

CALL TASKS tax_analysis ↗

Input Mappings (3)
Input Value
trained_classifier trained_classifier
representative_seqs_qza deblur.representative_seqs_qza
representative_table_qza deblur.representative_table_qza

Images

Container images used by tasks in this workflow:

🐳 Parameterized Image
⚙️ Parameterized

Configured via input:
docker

Used by 5 tasks:
  • qiime_import_from_bam
  • trim_reads
  • join_paired_ends
  • deblur
  • tax_analysis
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amplicon16S_analysis - WDL Source Code

version 1.0

#DX_SKIP_WORKFLOW

import "../tasks/tasks_16S_amplicon.wdl" as qiime 

workflow amplicon16S_analysis {
    
    meta {
        description: "Running 16S amplicon (from BAM format) sequencing analysis with qiime."
        author: "fnegrete"
        email:  "viral_ngs@broadinstitute.org"
        allowNestedInputs: true 
    }
    input {
        Array[File]    reads_bam
        File    trained_classifier
        Boolean keep_untrimmed_reads
    }

    call qiime.qiime_import_from_bam {
        input:
            reads_bam  = reads_bam
    }
    #__________________________________________
    call qiime.trim_reads {
        input:
           reads_qza            = qiime_import_from_bam.reads_qza,
           keep_untrimmed_reads = keep_untrimmed_reads
    }
    #__________________________________________
    call qiime.join_paired_ends {
        input: 
            trimmed_reads_qza = trim_reads.trimmed_reads_qza
    }
    #_________________________________________
    call qiime.deblur {
        input: 
            joined_end_reads_qza = join_paired_ends.joined_end_reads_qza
    }
    #_________________________________________
    call qiime.tax_analysis {
        input:
            trained_classifier = trained_classifier,
            representative_seqs_qza = deblur.representative_seqs_qza,
            representative_table_qza = deblur.representative_table_qza
    }
}