Quality Control Workflow

Quality Control Wdl

Description:

Description Text

Inputs:

• Assembly (filepath)
  • Local copy of assembly
• Sample Name (string)
• Read 1 (filepath)
• Read 2 (filepath)

Input JSON Template:

{

    "assembly_qc.assembly": "/path/to/assembly.fastq.gz",

    "assembly_qc.read1": "/path/to/read1.fastq.gz",

    "assembly_qc.read2": "/path/to/read2.fastq.gz",

    "assembly_qc.sample_name": "SampleName"

}

Output:

• Quast Report (File)
• Largest Contig Value (Int)
• Total Length Value (Int)
• N50 Value (Int)
• N90 Value (Int)
• L50 Value (Int)
• L90 Value (Int)
• Mash Ani (String)
• Mash Genus (String)
• Mash Species (String)
• Mash Subspecies (String)
• Mash Taxaid (String)
• Checkm Output (File)
• Checkm Markerlineage (String)
• Checkm Completeness (String)
• Checkm Contamination (String)
• Checkm Heterogeneity (String)
• Merqury Qv (String)
• Merqury Comp (String)
• Merqury Qv File (File)
• Merqury Completeness File (File)
• Merqury Version (String)
• Mlst Scheme (String)
• Mlst Seqtype (String)
• Mlst Alleles (String)
• FastQC R1 Html (File)
• FastQC R2 Html (File)
• FastQC R1 Pass Warn Fail (String)
• FastQC R2 Pass Warn Fail (String)
• FastQC R1 Total Sequences (String)
• FastQC R1 Total Bases (String)
• FastQC R1 Poor Quality (String)
• FastQC R1 Sequence Length (String)
• FastQC R1 Gc Content (String)
• FastQC R2 Total Sequences (String)
• FastQC R2 Total Bases (String)
• FastQC R2 Poor Quality (String)
• FastQC R2 Sequence Length (String)
• FastQC R2 Gc Content (String)
• FastQC Version (String)

Task Wdls

• MASH-Task