HUMAnN 3 workflow Version 1
Download RO-CrateRuns MetaPhlAn 4 and HUMAnN 3
- Optional short read quality control workflow (https://workflowhub.eu/workflows/336)
- Includes renormalizing and all regroupings to other functional categories (EC,KO.. etc)
Required inputs are paired end reads and databases.
Other UNLOCK workflows on WorkflowHub:
https://workflowhub.eu/projects/16/workflows?view=default
Tool CWL files and other workflows can be found at:
https://gitlab.com/m-unlock/cwl
Click and drag the diagram to pan, double click or use the controls to zoom.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| identifier | identifier used | Identifier for this dataset used in this workflow |
|
| threads | Number of threads | Number of threads to use for computational processes |
|
| memory | Memory usage (MB) | Maximum memory usage in megabytes (default 8000) |
|
| forward_reads | Forward reads | Forward sequence fastq file |
|
| reverse_reads | Reverse reads | Reverse sequence fastq file |
|
| skip_read_filter | Skip quality filtering | Skip quality filtering. (Default false) |
|
| humandb | Filter human reads | Bowtie2 index folder. Provide the folder in which the in index files are located. |
|
| reference_filter_db | Filter reference file(s) | Custom reference database for filtering with Hostile. Provide the folder in which the bowtie2 index files are located. (default false) |
|
| use_reference_mapped_reads | Use mapped reads | Use mapped reads mapped to the custom reference db. (Default false, discard mapped) |
|
| output_filtered_reads | Output filtered reads | Output filtered reads when filtering is applied. (Default false) |
|
| metaphlan4_bt2_database | MetaPhlAn4 database | MetaPhlAn4 database location |
|
| uniref_dbtype | UniRef database type | uniref50 or uniref90. Match this with your selected database! |
|
| humann3_nucleotide_database | HUMAnN3 nucleotide database | HUMAnN3 nucleotide database location |
|
| humann3_protein_database | HUMAnN3 protein database | HUMAnN3 protein database location |
|
| destination | Output Destination | Optional output destination only used for cwl-prov reporting. |
|
| source | Input URLs used for this run | A provenance element to capture the original source of the input data |
|
Steps
| ID | Name | Description |
|---|---|---|
| workflow_merge_reads | Merge paired reads | This is workflow specific step and creates a single file object. Also merges reads if multiple files are given. (not interleaving) |
| workflow_illumina_quality | Shortreads quality workflow | Quality and contamination filtering of short reads |
| interleave_fastq | Interleave fastq | Interleave QC forward and reverse files for subsequent tools |
| metaphlan | MetaPhlAn 4 | Profiling the composition of microbial communities |
| humann | HUMAnN 3 | HMP Unified Metabolic Analysis Network. |
| humann_unpack_pathways | Unpack pathways | HUMAnN 3 Unpack pathways |
| humann_renorm_table_genefamilies | Renorm gene families | HUMAnN 3 renormalize genefamilies |
| humann_renorm_table_pathways | Renorm pathways | HUMAnN 3 renormalize pathways |
| humann_regroup_table | Regroup unnormalized | HUMAnN 3 regroup genefamily |
| humann_regroup_renorm_table | Regroup renormalized | HUMAnN 3 regroup renormalized genefamilies |
| renorm_groups_to_array | Merge file arrays | Merges arrays of files in an array to an array of files |
| files_to_folder_normalized | Normalized tables | Normalized tables folder |
| out_fwd_reads | Output fwd reads | Step needed to output filtered reads because there is an option to not to. |
| out_rev_reads | Output rev reads | Step needed to output filtered reads because there is an option to not to. |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| humann_genefamilies_out | Gene families | HUMAnN 3 Gene families abundances |
|
| humann_pathabundance_out | Pathway abundances | HUMAnN 3 pathway abundances |
|
| humann_pathcoverage_out | Pathway coverage | HUMAnN 3 pathway coverage |
|
| humann_log_out | HUMAnN 3 log | HUMAnN 3 |
|
| humann_stdout_out | HUMAnN 3 stdout | HUMAnN 3 standard out |
|
| humann_pathways_unpacked | Pathways unpacked | HUMAnN 3 pathways gene abundances |
|
| regrouped_tables | Regrouped tables | Regrouped tabes unnormalized |
|
| normalized_tables | Normalized tables | Normalized tables Director |
|
| metaphlan_profile | MetaPhlAn4 profile | MetaPhlAn4 profile tsv |
|
| metaphlan_bt2out | MetaPhlAn4 bt2out | MetaPhlAn4 bowtie 2 output |
|
| QC_forward_reads | Filtered forward read | Filtered forward read |
|
| QC_reverse_reads | Filtered reverse read | Filtered reverse read |
|
| quality_reports | n/a | Quality reports output directory |
|
Version History
Version 1 (earliest) Created 6th Nov 2025 at 13:23 by Bart Nijsse
Initial commit
Open
masterf5c6daa
Creators and Submitter
Views: 1723 Downloads: 303
Created: 6th Nov 2025 at 13:23
Last updated: 23rd Jan 2026 at 10:22
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