Workflow (hybrid) metagenomic assembly and binning + GEMs
Accepts both Illumina and Long reads (ONT/PacBio)
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Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
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Workflow LongRead Quality: https://workflowhub.eu/workflows/337
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Kraken2 taxonomic classification of FASTQ reads
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SPAdes/Flye (Assembly)
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QUAST (Assembly quality report)
Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)
- Metabat2/MaxBin2/SemiBin
- DAS Tool
- CheckM
- BUSCO
- GTDB-Tk
Workflow Genome-scale metabolic models https://workflowhub.eu/workflows/372 (optional)
- CarveMe (GEM generation)
- MEMOTE (GEM test suite)
- SMETANA (Species METabolic interaction ANAlysis)
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here:
https://gitlab.com/m-unlock/cwl
How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
ID | Name | Description | Type |
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identifier | Identifier used | Identifier for this dataset used in this workflow |
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illumina_forward_reads | Forward reads | Forward sequence file path |
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illumina_reverse_reads | Reverse reads | Reverse sequence file path |
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pacbio_reads | PacBio reads | File with PacBio reads locally |
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nanopore_reads | PacBio reads | File with PacBio reads locally |
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filter_references | Contamination reference file | bbmap reference fasta file paths for contamination filtering |
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use_reference_mapped_reads | Keep mapped reads | Continue with reads mapped to the given reference |
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keep_filtered_reads | Keep filtered reads | Keep filtered reads in the final output |
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deduplicate | Deduplicate reads | Remove exact duplicate reads with fastp |
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kraken_database | Kraken2 database | Absolute path with database location of kraken2 |
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gtdbtk_data | gtdbtk data directory | Directory containing the GTDBTK repository |
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busco_data | BUSCO dataset | Path to the BUSCO dataset download location |
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ont_basecall_model | ONT Basecalling model | Basecalling model used with guppy default r941_min_high. Available: r941_trans, r941_flip213, r941_flip235, r941_min_fast, r941_min_high, r941_prom_fast, r941_prom_high. (required) |
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pilon_fixlist | Pilon fix list | A comma-separated list of categories of issues to try to fix |
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metagenome | When working with metagenomes | Metagenome option for assemblers |
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run_spades | Use SPAdes | Run with SPAdes assembler |
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run_flye | Use Flye | Run with Flye assembler |
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run_pilon | Use Pilon | Run with Pilon illumina assembly polishing |
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binning | Run binning workflow | Run with contig binning workflow |
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run_GEM | Run GEM workflow | Run the community genomescale metabolic models workflow on bins |
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run_smetana | Run SMETANA | Run SMETANA (Species METabolic interaction ANAlysis) |
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threads | Number of threads | Number of threads to use for computational processes |
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memory | Memory usage (MB) | Maximum memory usage in megabytes |
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destination | Output Destination (prov only) | Not used in this workflow. Output destination used for cwl-prov reporting only. |
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Steps
ID | Name | Description |
---|---|---|
workflow_quality_illumina | Quality and filtering workflow | Quality assessment of illumina reads with rRNA filtering option |
workflow_quality_nanopore | Nanopore quality and filtering workflow | Quality and filtering workflow for nanopore reads |
nanopore_kraken2 | Kraken2 Nanopore | Taxonomic classification of nanopore FASTQ reads |
illumina_kraken2 | Kraken2 Illumina | Taxonomic classification of illumina FASTQ reads |
kraken2_compress | Compress kraken2 | Compress large kraken2 report file |
kraken2_krona | Krona Kraken2 | Visualization of kraken2 with Krona |
spades | SPAdes assembly | Genome assembly using spades with illumina/pacbio reads |
compress_spades | SPAdes compressed | Compress the large Spades assembly output files |
flye | Nanopore Flye assembly | De novo assembly of single-molecule reads with Flye |
medaka | Medaka polishing of assembly | Medaka for polishing of assembled genome |
metaquast_medaka | assembly evaluation | evaluation of polished assembly with metaQUAST |
workflow_pilon | Pilon worklow | Illumina reads assembly polishing with Pilon |
metaquast_pilon | Illumina assembly evaluation | Illumina evaluation of pilon polished assembly with metaQUAST |
bbmap | BBmap read mapping | Illumina read mapping using BBmap on assembled contigs |
sam_to_sorted_bam | sam conversion to sorted bam | Sam file conversion to a sorted indexed bam file |
contig_read_counts | Samtools idxstats | Reports alignment summary statistics |
workflow_binning | Binning workflow | Binning workflow to create bins |
workflow_GEM | GEM workflow | CarveMe community genomescale metabolic models workflow from bins |
keep_readfilter_files_to_folder | Read filtering output folder | Preparation of read filtering output files to a specific output folder |
readfilter_files_to_folder | Read filtering output folder | Preparation of read filtering output files to a specific output folder |
kraken2_files_to_folder | Kraken2 output folder | Preparation of Kraken2 output files to a specific output folder |
spades_files_to_folder | SPADES output to folder | Preparation of SPAdes output files to a specific output folder |
flye_files_to_folder | Flye output folder | Preparation of Flye output files to a specific output folder |
metaquast_medaka_files_to_folder | Nanopore metaQUAST output folder | Preparation of metaQUAST output files to a specific output folder |
medaka_files_to_folder | Medaka output folder | Preparation of Medaka output files to a specific output folder |
metaquast_pilon_files_to_folder | Illumina metaQUAST output folder | Preparation of QUAST output files to a specific output folder |
pilon_files_to_folder | Pilon output folder | Preparation of pilon output files to a specific output folder |
assembly_files_to_folder | Flye output folder | Preparation of Flye output files to a specific output folder |
binning_files_to_folder | Binning output to folder | Preparation of binning output files and folders to a specific output folder |
GEM_files_to_folder | GEM workflow output to folder | Preparation of GEM workflow output files and folders to a specific output folder |
Outputs
ID | Name | Description | Type |
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read_filtering_output_keep | Read filtering output | Read filtering stats + filtered reads |
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read_filtering_output | Read filtering output | Read filtering stats + filtered reads |
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kraken2_output | Kraken2 reports | Kraken2 taxonomic classification reports |
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assembly_output | Assembly output | Output from different assembly steps |
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binning_output | Binning output | Binning outputfolders |
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gem_output | Community GEM output | Community GEM output folder |
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Version History
Version 1 (earliest) Created 14th Jun 2022 at 09:14 by Bart Nijsse
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Views: 2924 Downloads: 265
Created: 14th Jun 2022 at 09:14
Last updated: 7th Apr 2023 at 15:10
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