Metagenomics workflow
Version 1

Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflowquality.cwl: FastQC (control) fastp (trimming) - Kraken2 (Taxonomic Read Classification - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - samtobam (sam to indexed bam) - metabatContigDepths (jgisummarizebamcontig_depths) - MetaBat2 (binning) - SAPP (bin annotation)

Inputs

ID Name Description Type
filter_rrna Filter rRNA from reads n/a 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 maximum memory usage in megabytes maximum memory usage in megabytes int?
gzip n/a input data is gzip compressed boolean (Optional)
kraken_database n/a database location of kraken2 Directory
metagenomics metagenomics sample this flag is required for metagenomic sample data boolean?
isolate high-coverage mode this flag is highly recommended for high-coverage isolate and multi-cell data boolean?
pacbio_reads pacbio reads file with PacBio reads locally File[]?

Steps

ID Name Description
workflow_quality
workflow_kraken
workflow_spades
workflow_quast
workflow_bbmap
workflow_sam_to_sorted_bam
workflow_merge_bam_files
workflow_metabat_contig_depths
workflow_metabat
workflow_sapp
kraken_files_to_folder
spades_files_to_folder
quast_files_to_folder
sorted_bam_files_to_folder
metabat_files_to_folder
sapp_files_to_folder

Outputs

ID Name Description Type
x1 n/a n/a Directory[]
x2 n/a n/a Directory[]
x3 n/a n/a Directory
x4 n/a n/a Directory
x5 n/a n/a Directory
x6 n/a n/a Directory
x7 n/a n/a Directory
x8 n/a n/a Directory
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Views: 33   Downloads: 1

Created: 15th Oct 2020 at 14:55

Last used: 20th Oct 2020 at 17:57

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