Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[Kraken2] Update Krona to be compatible with viral data #709

Merged
merged 10 commits into from
Jan 24, 2025
Merged

[Kraken2] Update Krona to be compatible with viral data #709

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
5076c08
fix krona to be better
sage-wright Jan 2, 2025
a21a695
update relevant documentation
sage-wright Jan 2, 2025
e2cfffb
I FORGOT THE M IN HTML SMH WHAT A DISASTER
sage-wright Jan 2, 2025
8b7305f
reduce cpu count
sage-wright Jan 2, 2025
7ac53a4
add missing kraken2_ont
sage-wright Jan 3, 2025
780454d
remove unnecessary path
sage-wright Jan 6, 2025
6b65980
Merge branch 'main' into smw-krona-dev
sage-wright Jan 15, 2025
fb04f01
Merge branch 'main' into smw-krona-dev
sage-wright Jan 24, 2025
7f8a28e
fix up some documentation
sage-wright Jan 24, 2025
57883e0
fix language because it was wrong
sage-wright Jan 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file modified docs/assets/figures/example_krona_report.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
6 changes: 3 additions & 3 deletions docs/workflows/genomic_characterization/theiameta.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
|---|---|---|---|---|
| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |
| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB vX.X.X | Yes | Sample-level |

## TheiaMeta Workflows

Expand Down Expand Up @@ -57,11 +57,11 @@ The TheiaMeta_Illumina_PE workflow processes Illumina paired-end (PE) reads ge
| kraken2_raw | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 16 | Optional |
| krona_clean | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional |
| krona_clean | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
| krona_clean | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/biocontainers/krona:2.7.1--pl526_5 | Optional |
| krona_clean | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1 | Optional |
| krona_clean | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional |
| krona_raw | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional |
| krona_raw | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
| krona_raw | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/biocontainers/krona:2.7.1--pl526_5 | Optional |
| krona_raw | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1 | Optional |
| krona_raw | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional |
| metaspades | **kmers** | String | Kmer list to use with metaspades. If not provided metaspades automatically sets this value | | Optional |
| metaspades | **metaspades_opts** | String | Additional arguments to pass to metaspades task | | Optional |
Expand Down
8 changes: 3 additions & 5 deletions docs/workflows/standalone/kraken2.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

| **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** |
|---|---|---|---|---|
| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.3.0 | Yes | Sample-level |
| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB vX.X.X | Yes | Sample-level |

## Kraken2 Workflows

Expand Down Expand Up @@ -63,7 +63,7 @@ Besides the data input types, there are minimal differences between these two wo
| kraken2_pe or kraken2_se | **unclassified_out** | String | Allows user to rename unclassified FASTQ files output. Must include .fastq as the suffix | unclassified#.fastq | Optional | ONT, PE, SE |
| krona | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | PE, SE |
| krona | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | PE, SE |
| krona | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/biocontainers/krona:2.7.1--pl526_5 | Optional | PE, SE |
| krona | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/krona:2.8.1 | Optional | PE, SE |
| krona | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | PE, SE |
| kraken2_recalculate_abundances | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT |
| kraken2_recalculate_abundances | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT |
Expand Down Expand Up @@ -145,11 +145,9 @@ When assessing the taxonomic identity of a single isolate's sequence, it is norm

[Krona](https://github.com/marbl/Krona) produces an interactive report that allows hierarchical data, such as the one from Kraken2, to be explored with zooming, multi-layered pie charts. These pie charts are intuitive and highly responsive.

Krona will only output hierarchical results for bacterial organisms in its current implementation.

??? toggle "Example Krona report"

Below is an example of the `krona_html` for a metagenomic sample. Taxonomic rank is organised from the centre of the pie chart to the edge, with each slice representing the relative abundance of a given taxa in the sample.
Below is an example of the `krona_html` for a bacterial sample. Taxonomic rank is organised from the centre of the pie chart to the edge, with each slice representing the relative abundance of a given taxa in the sample.

![Example Krona Report](../../assets/figures/example_krona_report.png)

Expand Down
4 changes: 2 additions & 2 deletions docs/workflows_overview/workflows_alphabetically.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ title: Alphabetical Workflows
| [**Find_Shared_Variants**](../workflows/phylogenetic_construction/find_shared_variants.md)| Combines and reshapes variant data from Snippy_Variants to illustrate variants shared across multiple samples | Bacteria, Mycotics | Set-level | Yes | v2.0.0 | [Find_Shared_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Find_Shared_Variants_PHB:main?tab=info) |
| [**Freyja Workflow Series**](../workflows/genomic_characterization/freyja.md)| Recovers relative lineage abundances from mixed sample data and generates visualizations | SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.2.0 | [Freyja_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_FASTQ_PHB:main?tab=info), [Freyja_Plot_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Plot_PHB:main?tab=info), [Freyja_Dashboard_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Dashboard_PHB:main?tab=info), [Freyja_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Freyja_Update_PHB:main?tab=info) |
| [**GAMBIT_Query**](../workflows/standalone/gambit_query.md)| Taxon identification of genome assembly using GAMBIT | Bacteria, Mycotics | Sample-level | Yes | v2.0.0 | [Gambit_Query_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Gambit_Query_PHB:main?tab=info) |
| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.3.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | vX.X.X | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info), [Kraken2_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_ONT_PHB:main?tab=info) |
| [**kSNP3**](../workflows/phylogenetic_construction/ksnp3.md)| SNP-based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | vX.X.X | [kSNP3_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/kSNP3_PHB:main?tab=info) |
| [**Lyve_SET**](../workflows/phylogenetic_construction/lyve_set.md)| Alignment of reads to a reference genome, SNP calling, curation of high quality SNPs, phylogenetic analysis | Bacteria | Set-level | Yes | v2.1.0 | [Lyve_SET_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Lyve_SET_PHB:main?tab=info) |
| [**MashTree_FASTA**](../workflows/phylogenetic_construction/mashtree_fasta.md)| Mash-distance based phylogenetic analysis from assemblies | Bacteria, Mycotics, Viral | Set-level | Some optional features incompatible, Yes | vX.X.X | [MashTree_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/MashTree_FASTA_PHB:main?tab=info) |
Expand All @@ -45,7 +45,7 @@ title: Alphabetical Workflows
| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.3.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
| [**TheiaCov Workflow Series**](../workflows/genomic_characterization/theiacov.md) | Viral genome assembly, QC and characterization from amplicon sequencing | HIV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level, Set-level | Some optional features incompatible, Yes | vX.X.X | [TheiaCoV_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_PE_PHB:main?tab=info), [TheiaCoV_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_Illumina_SE_PHB:main?tab=info), [TheiaCoV_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ONT_PHB:main?tab=info), [TheiaCoV_ClearLabs_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_ClearLabs_PHB:main?tab=info), [TheiaCoV_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_PHB:main?tab=info), [TheiaCoV_FASTA_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaCoV_FASTA_Batch_PHB:main?tab=info)
| [**TheiaEuk**](../workflows/genomic_characterization/theiaeuk.md) | Mycotic genome assembly, QC and characterization from WGS data | Mycotics | Sample-level | Some optional features incompatible, Yes | vX.X.X | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.3.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | vX.X.X | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
| [**TheiaProk Workflow Series**](../workflows/genomic_characterization/theiaprok.md) | Bacterial genome assembly, QC and characterization from WGS data | Bacteria | Sample-level | Some optional features incompatible, Yes | vX.X.X | [TheiaProk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_PE_PHB:main?tab=info), [TheiaProk_Illumina_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_Illumina_SE_PHB:main?tab=info), [TheiaProk_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_ONT_PHB:main?tab=info), [TheiaProk_FASTA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaProk_FASTA_PHB:main?tab=info) |
| [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
| [**Transfer_Column_Content**](../workflows/data_export/transfer_column_content.md)| Transfer contents of a specified Terra data table column for many samples ("entities") to a GCP storage bucket location | Any taxa | Set-level | Yes | v1.3.0 | [Transfer_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Transfer_Column_Content_PHB:main?tab=info) |
Expand Down
4 changes: 2 additions & 2 deletions docs/workflows_overview/workflows_kingdom.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,12 @@ title: Workflows by Kingdom
| [**Concatenate_Illumina_Lanes**](../workflows/standalone/concatenate_illumina_lanes.md)| Concatenate Illumina lanes for a single sample | Any taxa | Sample-level | Yes | v2.3.0 | [Concatenate_Illumina_Lanes_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Illumina_Lanes_PHB:main?tab=info) |
| [**Create_Terra_Table**](../workflows/data_import/create_terra_table.md)| Upload data to Terra and then run this workflow to have the table automatically created | Any taxa | | Yes | v2.2.0 | [Create_Terra_Table_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Create_Terra_Table_PHB:main?tab=info) |
| [**Fetch_SRR_Accession**](../workflows/public_data_sharing/fetch_srr_accession.md)| Provided a BioSample accession, identify any associated SRR accession(s) | Any taxa | Sample-level | Yes | v2.3.0 | [Fetch_SRR_Accession_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Fetch_SRR_Accession_PHB:main?tab=info) |
| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | v2.3.0 | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info) |
| [**Kraken2**](../workflows/standalone/kraken2.md) | Taxa identification from reads | Any taxa | Sample-level | Yes | vX.X.X | [Kraken2_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_PE_PHB:main?tab=info), [Kraken2_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_SE_PHB:main?tab=info), [Kraken2_ONT_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Kraken2_ONT_PHB:main?tab=info) |
| [**NCBI_Scrub**](../workflows/standalone/ncbi_scrub.md)| Runs NCBI's HRRT on Illumina FASTQs | Any taxa | Sample-level | Yes | v2.2.1 | [NCBI_Scrub_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_PE_PHB:main?tab=info), [NCBI_Scrub_SE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/NCBI_Scrub_SE_PHB:main?tab=info) |
| [**RASUSA**](../workflows/standalone/rasusa.md)| Randomly subsample sequencing reads to a specified coverage | Any taxa | Sample-level | Yes | v2.0.0 | [RASUSA_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/RASUSA_PHB:main?tab=info) |
| [**Rename_FASTQ**](../workflows/standalone/rename_fastq.md)| Rename paired-end or single-end read files in a Terra data table in a non-destructive way | Any taxa | Sample-level | Yes | v2.1.0 | [Rename_FASTQ_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Rename_FASTQ_PHB:im-utilities-rename-files?tab=info) |
| [**SRA_Fetch**](../workflows/data_import/sra_fetch.md)| Import publicly available reads from SRA using SRR#, ERR# or DRR# | Any taxa | Sample-level | Yes | v2.2.0 | [SRA_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/SRA_Fetch_PHB:main?tab=info) |
| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | v2.3.0 | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
| [**TheiaMeta**](../workflows/genomic_characterization/theiameta.md) | Genome assembly and QC from metagenomic sequencing | Any taxa | Sample-level | Yes | vX.X.X | [TheiaMeta_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaMeta_Illumina_PE_PHB:main?tab=info) |
| [**TheiaValidate**](../workflows/standalone/theiavalidate.md)| This workflow performs basic comparisons between user-designated columns in two separate tables. | Any taxa | | No | v2.0.0 | [TheiaValidate_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaValidate_PHB:main?tab=info) |
| [**Transfer_Column_Content**](../workflows/data_export/transfer_column_content.md)| Transfer contents of a specified Terra data table column for many samples ("entities") to a GCP storage bucket location | Any taxa | Set-level | Yes | v1.3.0 | [Transfer_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Transfer_Column_Content_PHB:main?tab=info) |
| [**Zip_Column_Content**](../workflows/data_export/zip_column_content.md)| Zip contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Zip_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Zip_Column_Content_PHB:main?tab=info) |
Expand Down
Loading
Loading