Metagenomics workflow Version 1
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Download RO CrateWorkflow 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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An open infrastructure for exploring new horizons for research on microbial communities.
