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)
samtobam (sam to indexed bam)
metabatContigDepths (jgisummarizebamcontigdepths)
MetaBat2 (binning)
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 (Optional) |
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 |

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Views: 472 Downloads: 30
Created: 15th Oct 2020 at 14:55
Last updated: 8th Jan 2021 at 10:15
Last used: 7th Mar 2021 at 21:13

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Version History
Version 7 (latest) Created 8th Jan 2021 at 10:15 by Jasper Koehorst
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