[Kraken2] Split database from Kraken2 TheiaCoV task

docs/workflows/genomic_characterization/theiacov.md

@@ -217,19 +217,22 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
 | ivar_consensus | **stats_n_coverage_primtrim_disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | SE,PE | HIV, MPXV, WNV, rsv_a, rsv_b, sars-cov-2 |
 | ivar_consensus | **stats_n_coverage_primtrim_docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/samtools:1.15 | Optional | SE,PE | HIV, MPXV, WNV, rsv_a, rsv_b, sars-cov-2 |
 | ivar_consensus | **stats_n_coverage_primtrim_memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | SE,PE | HIV, MPXV, WNV, rsv_a, rsv_b, sars-cov-2 |
+| kraken2_dehosted | **classified_out** | String | Allows user to rename the classified FASTQ files output. Must include .fastq as the suffix | classified#.fastq | Optional | CL | sars-cov-2 |
 | kraken2_dehosted | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | CL | sars-cov-2 |
 | kraken2_dehosted | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | CL | sars-cov-2 |
-| kraken2_dehosted | **docker_image** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.0.8-beta_hv | Optional | CL | sars-cov-2 |
+| kraken2_dehosted | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.0.8-beta_hv | Optional | CL | sars-cov-2 |
 | kraken2_dehosted | **kraken2_db** | String | The database used to run Kraken2 | /kraken2-db | Optional | CL | sars-cov-2 |
 | kraken2_dehosted | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | CL | sars-cov-2 |
 | kraken2_dehosted | **read2** | File | Internal component, do not modify | | Do not modify, Optional | CL | sars-cov-2 |
+| kraken2_dehosted | **unclassified_out** | String | Allows user to rename the unclassified FASTQ files output. Must include .fastq as the suffix | unclassified#.fastq | Optional | CL | sars-cov-2 |
+| kraken2_raw | **classified_out** | String | Allows user to rename the classified FASTQ files output. Must include .fastq as the suffix | classified#.fastq | Optional | CL | sars-cov-2 |
 | kraken2_raw | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | CL | sars-cov-2 |
 | kraken2_raw | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | CL | sars-cov-2 |
-| kraken2_raw | **docker_image** | Int | Docker container used in this task | us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.0.8-beta_hv | Optional | CL | sars-cov-2 |
+| kraken2_raw | **docker** | Int | Docker container used in this task | us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.0.8-beta_hv | Optional | CL | sars-cov-2 |
 | kraken2_raw | **kraken2_db** | String | The database used to run Kraken2 | /kraken2-db | Optional | CL | sars-cov-2 |
 | kraken2_raw | **memory** | String | Amount of memory/RAM (in GB) to allocate to the task | 8 | Optional | CL | sars-cov-2 |
-| kraken2_raw | **read_processing** | String | The tool used for trimming of primers from reads. Options are trimmomatic and fastp | trimmomatic | Optional | | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
 | kraken2_raw | **read2** | File | Internal component, do not modify | | Do not modify, Optional | CL | sars-cov-2 |
+| kraken2_raw | **unclassified_out** | String | Allows user to rename the unclassified FASTQ files output. Must include .fastq as the suffix | unclassified#.fastq | Optional | CL | sars-cov-2 |
 | nanoplot_clean | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
 | nanoplot_clean | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
 | nanoplot_clean | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/nanoplot:1.40.0 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
@@ -373,6 +376,7 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
 | workflow name | **flu_segment** | String | Influenza genome segment being analyzed. Options: "HA" or "NA". | HA | Optional, Required | FASTA | |
 | workflow name | **flu_subtype** | String | The influenza subtype being analyzed. Options: "Yamagata", "Victoria", "H1N1", "H3N2", "H5N1". Automatically determined. | | Optional | FASTA | |
 | workflow name | **genome_length** | Int | Use to specify the expected genome length | | Optional | FASTA, ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
+| workflow name | **kraken_db** | File | A Kraken2 database in .tar.gz format. Must contain viral and human sequences. | gs://theiagen-large-public-files-rp/terra/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz | Optional | CL, ONT, PE, SE |  HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
 | workflow name | **max_genome_length** | Int | Maximum genome length able to pass read screening | 2673870 | Optional | ONT, PE, SE | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
 | workflow name | **max_length** | Int | Maximum length for a read based on the SARS-CoV-2 primer scheme | 700 | Optional | ONT | HIV, MPXV, WNV, flu, rsv_a, rsv_b, sars-cov-2 |
 | workflow name | **medaka_docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019:1.3.0-medaka-1.4.3 | Optional | CL | |
@@ -1035,16 +1039,17 @@ All TheiaCoV Workflows (not TheiaCoV_FASTA_Batch)
 | ivar_vcf | File | iVar tsv output converted to VCF format | PE, SE |
 | ivar_version_consensus | String | Version of iVar for running the iVar consensus command | PE, SE |
 | ivar_version_primtrim | String | Version of iVar for running the iVar trim command | PE, SE |
-| kraken_human | Float | Percent of human read data detected using the Kraken2 software | CL, ONT, PE, SE |
-| kraken_human_dehosted | Float | Percent of human read data detected using the Kraken2 software after host removal | CL, ONT, PE |
-| kraken_report | File | Full Kraken report | CL, ONT, PE, SE |
-| kraken_report_dehosted | File | Full Kraken report after host removal | CL, ONT, PE |
-| kraken_sc2 | Float | Percent of SARS-CoV-2 read data detected using the Kraken2 software | CL, ONT, PE, SE |
-| kraken_sc2_dehosted | Float | Percent of SARS-CoV-2 read data detected using the Kraken2 software after host removal | CL, ONT, PE |
-| kraken_target_organism | String | Percent of target organism read data detected using the Kraken2 software | CL, ONT, PE, SE |
-| kraken_target_organism_dehosted | String | Percent of target organism read data detected using the Kraken2 software after host removal | CL, ONT, PE |
-| kraken_target_organism_name | String | The name of the target organism; e.g., "Monkeypox" or "Human immunodeficiency virus" | CL, ONT, PE, SE |
-| kraken_version | String | Version of Kraken software used | CL, ONT, PE, SE |
+| kraken2_database | String | Database file used for Kraken2 analysis | CL, ONT, PE, SE |
+| kraken2_human | Float | Percent of human read data detected using the Kraken2 software | CL, ONT, PE, SE |
+| kraken2_human_dehosted | Float | Percent of human read data detected using the Kraken2 software after host removal | CL, ONT, PE |
+| kraken2_report | File | Full Kraken report | CL, ONT, PE, SE |
+| kraken2_report_dehosted | File | Full Kraken report after host removal | CL, ONT, PE |
+| kraken2_sc2 | String | Percent of SARS-CoV-2 read data detected using the Kraken2 software | CL, ONT, PE, SE |
+| kraken2_sc2_dehosted | String | Percent of SARS-CoV-2 read data detected using the Kraken2 software after host removal | CL, ONT, PE |
+| kraken2_target_organism | String | Percent of target organism read data detected using the Kraken2 software | CL, ONT, PE, SE |
+| kraken2_target_organism_dehosted | String | Percent of target organism read data detected using the Kraken2 software after host removal | CL, ONT, PE |
+| kraken2_target_organism_name | String | The name of the target organism; e.g., "Monkeypox" or "Human immunodeficiency virus" | CL, ONT, PE, SE |
+| kraken2_version | String | Version of Kraken software used | CL, ONT, PE, SE |
 | meanbaseq_trim | Float | Mean quality of the nucleotide basecalls aligned to the reference genome after primer trimming | CL, ONT, PE, SE |
 | meanmapq_trim | Float | Mean quality of the mapped reads to the reference genome after primer trimming | CL, ONT, PE, SE |
 | medaka_reference | String | Reference sequence used in medaka task | CL, ONT |

docs/workflows/standalone/kraken2.md

@@ -33,10 +33,11 @@ Besides the data input types, there are minimal differences between these two wo
 | Database name | Database Description | Suggested Applications | GCP URI (for usage in Terra) | Source | Database Size (GB) | Date of Last Update |
 | --- | --- | --- | --- | --- | --- | --- |
 | **Kalamari v5.1** | Kalamari is a database of complete public assemblies, that has been fine-tuned for enteric pathogens and is backed by trusted institutions. [Full list available here ( in chromosomes.tsv and plasmids.tsv)](https://github.com/lskatz/Kalamari/tree/master/src) | Single-isolate enteric bacterial pathogen analysis (Salmonella, Escherichia, Shigella, Listeria, Campylobacter, Vibrio, Yersinia) | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/kraken2.kalamari_5.1.tar.gz`** | ‣ | 1.5 | 18/5/2022 |
-| **standard 8GB** | Standard RefSeq database (archaea, bacteria, viral, plasmid, human, UniVec_Core) capped at 8GB | Prokaryotic or viral organisms, but for enteric pathogens, we recommend Kalamari | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/k2_standard_08gb_20240112.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 7.5 | 12/1/2024 |
-| **standard 16GB** | Standard RefSeq database (archaea, bacteria, viral, plasmid, human, UniVec_Core) capped at 16GB | Prokaryotic or viral organisms, but for enteric pathogens, we recommend Kalamari | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/k2_standard_16gb_20240112.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 15 | 12/1/2024 |
 | **standard** | Standard RefSeq database (archaea, bacteria, viral, plasmid, human, UniVec_Core)  | Prokaryotic or viral organisms, but for enteric pathogens, we recommend Kalamari | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/k2_standard_20240112.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 72 | 18/4/2023 |
+| **standard 16GB** | Standard RefSeq database (archaea, bacteria, viral, plasmid, human, UniVec_Core) capped at 16GB | Prokaryotic or viral organisms, but for enteric pathogens, we recommend Kalamari | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/k2_standard_16gb_20240112.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 15 | 12/1/2024 |
+| **standard 8GB** | Standard RefSeq database (archaea, bacteria, viral, plasmid, human, UniVec_Core) capped at 8GB | Prokaryotic or viral organisms, but for enteric pathogens, we recommend Kalamari | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/k2_standard_08gb_20240112.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 7.5 | 12/1/2024 |
 | **viral** | RefSeq viral | Viral metagenomics | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/k2_viral_20240112.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 0.6 | 12/1/2024 |
+| **viral with human** | Refseq viral plus human (GRCh38) | Viral metagenomics | **`gs://theiagen-large-public-files-rp/terra/databases/kraken2/kraken2_humanGRCh38_viralRefSeq_20240828.tar.gz`** | Theiagen Genomics | 2.76 | 10/7/2024 |
 | **EuPathDB48** | Eukaryotic pathogen genomes with contaminants removed. [Full list available here](https://genome-idx.s3.amazonaws.com/kraken/k2_eupathdb48_20201113/EuPathDB48_Contents.txt) | Eukaryotic organisms (Candida spp., Aspergillus spp., etc) | **`gs://theiagen-public-files-rp/terra/theiaprok-files/k2_eupathdb48_20201113.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 30.3 | 13/11/2020 |
 | **EuPathDB48** | Eukaryotic pathogen genomes with contaminants removed. [Full list available here](https://genome-idx.s3.amazonaws.com/kraken/k2_eupathdb48_20201113/EuPathDB48_Contents.txt) | Eukaryotic organisms (Candida spp., Aspergillus spp., etc) | **`gs://theiagen-large-public-files-rp/terra/databases/kraken/k2_eupathdb48_20230407.tar.gz`** | https://benlangmead.github.io/aws-indexes/k2 | 11 | 7/4/2023 |
 
@@ -48,13 +49,13 @@ Besides the data input types, there are minimal differences between these two wo
 | *workflow_name | **read1** | File |  |  | Required | ONT, PE, SE |
 | *workflow_name | **read2** | File |  |  | Required for PE only | PE |
 | *workflow_name | **samplename** | String |  |  | Required | ONT, PE, SE |
-| kraken2_pe or kraken2_se | **classified_out** | String | Allows user to rename the classified FASTQ files output. Must include .fastq as the suffix | classified#.fastq | Optional | ONT, PE, SE |
-| kraken2_pe or kraken2_se | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT, PE, SE |
-| kraken2_pe or kraken2_se | **disk_size** | Int | GB of storage to request for VM used to run the kraken2 task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database) | 100 | Optional | ONT, PE, SE |
-| kraken2_pe or kraken2_se | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db | Optional | ONT, PE, SE |
-| kraken2_pe or kraken2_se | **kraken2_args** | String | Allows a user to supply additional kraken2 command-line arguments |  | Optional | ONT, PE, SE |
-| kraken2_pe or kraken2_se | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 32 | Optional | ONT, PE, SE |
-| 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 |
+| kraken2 | **classified_out** | String | Allows user to rename the classified FASTQ files output. Must include .fastq as the suffix | classified#.fastq | Optional | ONT, PE, SE |
+| kraken2 | **cpu** | Int | Number of CPUs to allocate to the task | 4 | Optional | ONT, PE, SE |
+| kraken2 | **disk_size** | Int | GB of storage to request for VM used to run the kraken2 task. Increase this when using large (>30GB kraken2 databases such as the "k2_standard" database) | 100 | Optional | ONT, PE, SE |
+| kraken2 | **docker** | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/staphb/kraken2:2.1.2-no-db | Optional | ONT, PE, SE |
+| kraken2 | **kraken2_args** | String | Allows a user to supply additional kraken2 command-line arguments |  | Optional | ONT, PE, SE |
+| kraken2 | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 32 | Optional | ONT, PE, SE |
+| kraken2 | **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 |
@@ -133,7 +134,13 @@ 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.
+!!! warning
+
+    Krona will only output hierarchical results for **bacterial organisms** in its current implementation.
+
+!!! warning
+
+    Krona is only available for Kraken reports generated with **Illumina data**, paired or singled-ended.
 
 ??? toggle "Example Krona report"
 
@@ -146,4 +153,11 @@ Krona will only output hierarchical results for bacterial organisms in its curre
     | --- | --- |
     | Software Source Code | [Kraken2 on GitHub](https://github.com/DerrickWood/kraken2/)  |
     | Software Documentation | <https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown> |
-    | Original Publication(s) | [Improved metagenomic analysis with Kraken 2](https://link.springer.com/article/10.1186/s13059-019-1891-0) |
+    | Original Publication(s) | [Improved metagenomic analysis with Kraken 2](https://link.springer.com/article/10.1186/s13059-019-1891-0) |
+
+!!! techdetails "Krona Technical Details"
+    |  | Links |
+    | --- | --- |
+    | Software Source Code | [Krona on GitHub](https://github.com/marbl/Krona)  |
+    | Software Documentation | <https://github.com/marbl/Krona/wiki> |
+    | Original Publication(s) | [Interactive metagenomic visualization in a Web browser](https://doi.org/10.1186/1471-2105-12-385) |