Workflow Type: Common Workflow Language
Work-in-progress

Workflow for Metagenomics from raw reads to annotated bins. Steps:

  • workflow_quality.cwl:
    • FastQC (control)
    • fastp (trimming)
  • Kraken2 (Taxonomic Read Classification
  • SPAdes (Assembly)
  • QUAST (Assembly quality report)
  • BBmap (Read mapping to assembly)
  • sam_to_bam (sam to indexed bam)
  • metabatContigDepths (jgi_summarize_bam_contig_depths)
  • MetaBat2 (binning)

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Inputs

ID Name Description Type
filter_rrna rRNA filtering rRNA read filtering using ...
  • boolean
forward_reads forward reads forward sequence file locally
  • File[]
reverse_reads reverse reads reverse sequence file locally
  • File[]
threads number of threads number of threads to use for computational processes
  • int?
memory memory usage (mb) maximum memory usage in megabytes
  • int?
gzip gzip compression input data is gzip compressed
  • boolean
kraken_database Kraken2 database database location of kraken2
  • string
pacbio_reads pacbio reads file with PacBio reads locally
  • File[]?

Steps

ID Name Description
workflow_quality Quality and filtering workflow Quality assessment of illumina reads with rRNA filtering option
workflow_kraken Kraken2 workflow Read classification using the kraken2 database
workflow_spades SPADES assembly Genome assembly using spades with illumina/pacbio reads
workflow_quast Quast workflow Genome assembly quality assessment using Quast
workflow_bbmap bbmap read mapping illumina read mapping using BBmap
workflow_sam_to_sorted_bam sam conversion to sorted bam sam file conversion to a sorted indexed bam file
workflow_merge_bam_files Merging bam files Merge multiple bam files obtained from the sam to bam conversion module
workflow_metabat_contig_depths depth file from metabat2 Execution of metabat2 to obtain the depth file used in the binning process
workflow_metabat binning process Binning procedure using metabat2
kraken_files_to_folder Kraken output Preparation of kraken output files to a specific output folder
spades_files_to_folder SPADES output Preparation of spades output files to a specific output folder
quast_files_to_folder QUAST output Preparation of quast output files to a specific output folder
sorted_bam_files_to_folder BAM output Preparation of bam files output to a specific output folder
metabat_files_to_folder metabat output Preparation of metabatt output files to a specific output folder

Outputs

ID Name Description Type
fastqc_output FASTQC Quality reporting by FASTQC
  • Directory[]
filter_output Filtered reads Reads filtered output folder
  • Directory[]
kraken2_output KRAKEN2 Classification output folder by kraken
  • Directory
spades_output SPADES Metagenome assembly output by SPADES
  • Directory
quast_output QUAST Quast analysis output folder
  • Directory
bam_output BAM files Mapping results in indexed BAM format
  • Directory
metabat2_output MetaBat2 MetaBat2 output directory
  • Directory

Version History

Version 11 (latest) Created 18th Oct 2021 at 10:49 by Jasper Koehorst

Added more binning and assembly reports


Open master d4c912c

Version 10 Created 7th Jun 2021 at 18:34 by Jasper Koehorst

No revision comments

Frozen master c2519b1

Version 9 Created 1st Jun 2021 at 11:43 by Jasper Koehorst

No revision comments

Frozen master d6fcbfa

Version 8 Created 6th May 2021 at 07:03 by Jasper Koehorst

No revision comments

Frozen master 0660405

Version 7 Created 8th Jan 2021 at 10:15 by Jasper Koehorst

No revision comments

Frozen master f3919f2
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Views: 9579   Downloads: 987

Created: 15th Oct 2020 at 14:55

Last updated: 2nd Nov 2022 at 15:29

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