+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| lyveset_workflow | **dataset_name** | String | Free text string used to label output files | | Required |
@@ -45,6 +47,8 @@ The Lyve_SET WDL workflow runs the [Lyve-SET](https://github.com/lskatz/lyve-SET
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Workflow Actions
The Lyve_SET WDL workflow is run using read data from a set of samples. The workflow will produce a pairwise SNP matrix for the sample set and a maximum likelihood phylogenetic tree. Details regarding the default implementation of Lyve_SET and optional modifications are listed below.
diff --git a/docs/workflows/phylogenetic_construction/mashtree_fasta.md b/docs/workflows/phylogenetic_construction/mashtree_fasta.md
index 54751e398..d8d5e79b5 100644
--- a/docs/workflows/phylogenetic_construction/mashtree_fasta.md
+++ b/docs/workflows/phylogenetic_construction/mashtree_fasta.md
@@ -16,6 +16,8 @@ This workflow also features an optional module, `summarize_data`, that creates a
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| mashtree_fasta | **assembly_fasta** | Array[File] | The set of assembly fastas | | Required |
@@ -49,6 +51,8 @@ This workflow also features an optional module, `summarize_data`, that creates a
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Workflow Actions
`MashTree_Fasta` is run on a set of assembly fastas and creates a phylogenetic tree and matrix. These outputs are passed to a task that will rearrange the matrix to match the order of the terminal ends in the phylogenetic tree.
@@ -63,6 +67,8 @@ By default, this task appends a Phandango coloring tag to color all items from t
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| mashtree_docker | String | The Docker image used to run the mashtree task |
@@ -74,6 +80,8 @@ By default, this task appends a Phandango coloring tag to color all items from t
| mashtree_wf_analysis_date | String | The date the workflow was run |
| mashtree_wf_version | String | The version of PHB the workflow is hosted in |
+
+
## References
> Katz, L. S., Griswold, T., Morrison, S., Caravas, J., Zhang, S., den Bakker, H.C., Deng, X., and Carleton, H. A., (2019). Mashtree: a rapid comparison of whole genome sequence files. Journal of Open Source Software, 4(44), 1762,
diff --git a/docs/workflows/phylogenetic_construction/snippy_streamline.md b/docs/workflows/phylogenetic_construction/snippy_streamline.md
index 744b59482..ed70f28be 100644
--- a/docs/workflows/phylogenetic_construction/snippy_streamline.md
+++ b/docs/workflows/phylogenetic_construction/snippy_streamline.md
@@ -65,6 +65,8 @@ To run Snippy_Streamline, either a reference genome must be provided (`reference
- Using the core genome
- `core_genome` = true (as default)
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| snippy_streamline | **read1** | Array[File] | The forward read files | | Required |
@@ -133,6 +135,8 @@ To run Snippy_Streamline, either a reference genome must be provided (`reference
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Workflow Tasks
For automatic reference selection by the workflow (optional):
@@ -179,6 +183,8 @@ For all cases:
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| snippy_centroid_docker | String | Docker file used for Centroid |
@@ -223,3 +229,5 @@ For all cases:
| snippy_variants_snippy_docker | Array[String] | Docker file used for Snippy in the Snippy_Variants subworkfow |
| snippy_variants_snippy_version | Array[String] | Version of Snippy_Tree subworkflow used |
| snippy_wg_snp_matrix | File | CSV file of whole genome pairwise SNP distances between samples, calculated from the final alignment |
+
+
\ No newline at end of file
diff --git a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md
index 11f482891..0e9680518 100644
--- a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md
+++ b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md
@@ -39,6 +39,8 @@ The `Snippy_Streamline_FASTA` workflow is an all-in-one approach to generating a
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| snippy_streamline_fasta | **assembly_fasta** | Array[File] | The assembly files for your samples | | Required |
@@ -107,8 +109,12 @@ The `Snippy_Streamline_FASTA` workflow is an all-in-one approach to generating a
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| snippy_centroid_docker | String | Docker file used for Centroid |
@@ -151,3 +157,5 @@ The `Snippy_Streamline_FASTA` workflow is an all-in-one approach to generating a
| snippy_variants_snippy_docker | Array[String] | Docker file used for Snippy in the Snippy_Variants subworkfow |
| snippy_variants_snippy_version | Array[String] | Version of Snippy_Tree subworkflow used |
| snippy_wg_snp_matrix | File | CSV file of whole genome pairwise SNP distances between samples, calculated from the final alignment |
+
+
diff --git a/docs/workflows/phylogenetic_construction/snippy_tree.md b/docs/workflows/phylogenetic_construction/snippy_tree.md
index 86a19304c..4c9c7b02b 100644
--- a/docs/workflows/phylogenetic_construction/snippy_tree.md
+++ b/docs/workflows/phylogenetic_construction/snippy_tree.md
@@ -53,6 +53,8 @@ Sequencing data used in the Snippy_Tree workflow must:
- Using the core genome
- `core_genome` = true (as default)
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| snippy_tree_wf | **tree_name_updated** | String | Internal component, do not modify. Used for replacing spaces with underscores_ | | Do not modify |
@@ -123,6 +125,8 @@ Sequencing data used in the Snippy_Tree workflow must:
| wg_snp_dists | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 50 | Optional |
| wg_snp_dists | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 2 | Optional |
+
+
### Workflow Tasks
??? task "Snippy"
@@ -308,6 +312,8 @@ Sequencing data used in the Snippy_Tree workflow must:
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| snippy_cg_snp_matrix | File | CSV file of core genome pairwise SNP distances between samples, calculated from the final alignment |
@@ -336,6 +342,8 @@ Sequencing data used in the Snippy_Tree workflow must:
| snippy_tree_version | String | Version of Snippy_Tree workflow |
| snippy_wg_snp_matrix | File | CSV file of whole genome pairwise SNP distances between samples, calculated from the final alignment |
+
+
## References
> **Gubbins:** Croucher, Nicholas J., Andrew J. Page, Thomas R. Connor, Aidan J. Delaney, Jacqueline A. Keane, Stephen D. Bentley, Julian Parkhill, and Simon R. Harris. 2015. "Rapid Phylogenetic Analysis of Large Samples of Recombinant Bacterial Whole Genome Sequences Using Gubbins." Nucleic Acids Research 43 (3): e15.
diff --git a/docs/workflows/phylogenetic_construction/snippy_variants.md b/docs/workflows/phylogenetic_construction/snippy_variants.md
index b1fc18885..b62d1fbb3 100644
--- a/docs/workflows/phylogenetic_construction/snippy_variants.md
+++ b/docs/workflows/phylogenetic_construction/snippy_variants.md
@@ -29,6 +29,8 @@ The `Snippy_Variants` workflow aligns single-end or paired-end reads (in FASTQ f
!!! info "Query String"
The query string can be a gene or any other annotation that matches the GenBank file/output VCF **EXACTLY**
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| snippy_variants_wf | **reference_genome_file** | File | Reference genome (GenBank file or fasta) | | Required |
@@ -54,6 +56,8 @@ The `Snippy_Variants` workflow aligns single-end or paired-end reads (in FASTQ f
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Workflow Tasks
`Snippy_Variants` uses the snippy tool to align reads to the reference and call SNPs, MNPs and INDELs according to optional input parameters. The output includes a file of variants that is then queried using the `grep` bash command to identify any mutations in specified genes or annotations of interest. The query string MUST match the gene name or annotation as specified in the GenBank file and provided in the output variant file in the `snippy_results` column.
@@ -66,6 +70,8 @@ The `Snippy_Variants` workflow aligns single-end or paired-end reads (in FASTQ f
!!! warning "Note on coverage calculations"
The outputs from `samtools coverage` (found in the `snippy_variants_coverage_tsv` file) may differ from the `snippy_variants_percent_ref_coverage` due to different calculation methods. `samtools coverage` computes genome-wide coverage metrics (e.g., the proportion of bases covered at depth ≥ 1), while `snippy_variants_percent_ref_coverage` uses a user-defined minimum coverage threshold (default is 10), calculating the proportion of the reference genome with a depth greater than or equal to this threshold.
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| snippy_variants_bai | File | Indexed bam file of the reads aligned to the reference |
@@ -85,3 +91,5 @@ The `Snippy_Variants` workflow aligns single-end or paired-end reads (in FASTQ f
| snippy_variants_summary | File | A summary TXT fie showing the number of mutations identified for each mutation type |
| snippy_variants_version | String | Version of Snippy used |
| snippy_variants_wf_version | String | Version of Snippy_Variants used |
+
+
\ No newline at end of file
diff --git a/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md b/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md
index 308b02b60..92447e25e 100644
--- a/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md
+++ b/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md
@@ -17,6 +17,8 @@ However, nextclade can be used on any organism as long as an an existing, high-q
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| nextclade_addToRefTree | **assembly_fasta** | File | A fasta file with query sequence(s) to be placed onto the global tree | | Required |
@@ -34,8 +36,12 @@ However, nextclade can be used on any organism as long as an an existing, high-q
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| treeUpdate_auspice_json | File | Phylogenetic tree with user placed samples |
@@ -45,3 +51,5 @@ However, nextclade can be used on any organism as long as an an existing, high-q
| treeUpdate_nextclade_version | String | Nextclade version used |
| samples_to_ref_tree_analysis_date | String | Date of analysis |
| samples_to_ref_tree_version | String | Version of the Public Health Bioinformatics (PHB) repository used |
+
+
diff --git a/docs/workflows/phylogenetic_placement/usher.md b/docs/workflows/phylogenetic_placement/usher.md
index b2a016b42..ffe0cf1be 100644
--- a/docs/workflows/phylogenetic_placement/usher.md
+++ b/docs/workflows/phylogenetic_placement/usher.md
@@ -14,6 +14,8 @@
While this workflow is technically a set-level workflow, it works on the sample-level too. When run on the set-level, the samples are placed with respect to each other.
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| usher_workflow | **assembly_fasta** | Array[File] | The assembly files for the samples you want to place on the pre-existing; can either be a set of samples, an individual sample, or multiple individual samples | | Required |
@@ -29,8 +31,12 @@ While this workflow is technically a set-level workflow, it works on the sample-
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| usher_clades | File | The clades predicted for the samples |
@@ -41,3 +47,5 @@ While this workflow is technically a set-level workflow, it works on the sample-
| usher_subtrees | Array[File] | An array of subtrees where your samples have been placed |
| usher_uncondensed_tree | File | The entire global tree with your samples included (warning: may be a very large file if the organism is "sars-cov-2") |
| usher_version | String | The version of UShER used |
+
+
diff --git a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md
index 77efad884..459d3be88 100644
--- a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md
+++ b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md
@@ -52,7 +52,7 @@ To help users collect all required metadata, we have created the following Excel
The `using_clearlabs_data` and `using_reads_dehosted` arguments change the default values for the `read1_column_name`, `assembly_fasta_column_name`, and `assembly_mean_coverage_column_name` metadata columns. The default values are shown in the table below in addition to what they are changed to depending on what arguments are used.
- | Variable | Default Value | with `using_clearlabs_data` | with `using_reads_dehosted` | with both `using_clearlabs_data` ***and*** `using_reads_dehosted` |
+ | Variable | Default Value | with `using_clearlabs_data` | with `using_reads_dehosted` | with both `using_clearlabs_data` **_and_** `using_reads_dehosted` |
| --- | --- | --- | --- | --- |
| `read1_column_name` | `"read1_dehosted"` | `"clearlabs_fastq_gz"` | `"reads_dehosted"` | `"reads_dehosted"` |
| `assembly_fasta_column_name` | `"assembly_fasta"` | `"clearlabs_fasta"` | `"assembly_fasta"` | `"clearlabs_fasta"` |
@@ -60,14 +60,19 @@ To help users collect all required metadata, we have created the following Excel
### Inputs
+!!! tip "Use the sample table for the `terra_table_name` input"
+ Make sure your entry for `terra_table_name` is for the _sample_ table! While the root entity needs to be the set table, the input value for `terra_table_name` should be the sample table.
+
This workflow runs on the set-level.
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| mercury_prep_n_batch | **gcp_bucket_uri** | String | Google bucket where your SRA reads will be temporarily stored before transferring to SRA. Example: "gs://theiagen_sra_transfer" | | Required |
| mercury_prep_n_batch | **sample_names** | Array[String] | The samples you want to submit | | Required |
-| mercury_prep_n_batch | **terra_project_name** | String | The name of your Terra project. You can find this information in the URL of the webpage of your Terra dashboard. For example, if your URL contains #workspaces/example/my_workspace/ then your project name is example | | Required |
-| mercury_prep_n_batch | **terra_table_name** | String | The name of the Terra table where your samples can be found. Do not include the entity: prefix or the _id suffix, just the name of the table as listed in the sidebar on lefthand side of the Terra Data tab. | | Required |
+| mercury_prep_n_batch | **terra_project_name** | String | The name of your Terra project. You can find this information in the URL of the webpage of your Terra dashboard. For example, if your URL contains `#workspaces/example/my_workspace/` then your project name is `example` | | Required |
+| mercury_prep_n_batch | **terra_table_name** | String | The name of the Terra table where your **samples** can be found. Do not include the `entity:` prefix, the `_id` suffix, or the `_set_id` suffix, just the name of the sample-level data table as listed in the sidebar on lefthand side of the Terra Data tab. | | Required |
| mercury_prep_n_batch | **terra_workspace_name** | String | The name of your Terra workspace where your samples can be found. For example, if your URL contains #workspaces/example/my_workspace/ then your project name is my_workspace | | Required |
| download_terra_table | **cpu** | Int | Number of CPUs to allocate to the task | 1 | Optional |
| download_terra_table | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 10 | Optional |
@@ -101,8 +106,12 @@ This workflow runs on the set-level.
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| bankit_sqn_to_email | File | **Only for mpox submission**: the sqn file that you will use to submit mpox assembly files to NCBI via email |
@@ -117,6 +126,8 @@ This workflow runs on the set-level.
| mercury_script_version | String | Version of the Mercury tool that was used in this workflow |
| sra_metadata | File | SRA metadata TSV file for upload |
+
+
???+ toggle "An example excluded_samples.tsv file"
##### An example excluded_samples.tsv file {#example-excluded-samples}
diff --git a/docs/workflows/public_data_sharing/terra_2_gisaid.md b/docs/workflows/public_data_sharing/terra_2_gisaid.md
index 902521641..888177500 100644
--- a/docs/workflows/public_data_sharing/terra_2_gisaid.md
+++ b/docs/workflows/public_data_sharing/terra_2_gisaid.md
@@ -28,6 +28,8 @@ The optional variable `frameshift_notification` has three options that correspon
This workflow runs on the sample level.
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| Terra_2_GISAID | **client_id** | String | This value should be filled with the client-ID provided by GISAID | | Required |
@@ -43,8 +45,12 @@ This workflow runs on the sample level.
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| failed_uploads | Boolean | The metadata for any failed uploads |
@@ -52,3 +58,5 @@ This workflow runs on the sample level.
| gisaid_logs | File | The log files regarding the submission |
| terra_2_gisaid_analysis_date | String | The date of the analysis |
| terra_2_gisaid_version | String | The version of the PHB repository that this workflow is hosted in |
+
+
diff --git a/docs/workflows/public_data_sharing/terra_2_ncbi.md b/docs/workflows/public_data_sharing/terra_2_ncbi.md
index ac09caae8..0fa48e50e 100644
--- a/docs/workflows/public_data_sharing/terra_2_ncbi.md
+++ b/docs/workflows/public_data_sharing/terra_2_ncbi.md
@@ -103,6 +103,8 @@ This workflow runs on set-level data tables.
!!! info "Production Submissions"
Please note that an optional Boolean variable, `submit_to_production`, is **required** for a production submission.
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
| --- | --- | --- | --- | --- | --- |
| Terra_2_NCBI | **bioproject** | String | BioProject accession that the samples will be submitted to | | Required |
@@ -143,6 +145,8 @@ This workflow runs on set-level data tables.
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
??? task "Workflow Tasks"
##### Workflow Tasks {#workflow-tasks}
@@ -178,6 +182,8 @@ If the workflow ends unsuccessfully, no outputs will be shown on Terra and the `
The output files contain information mostly for debugging purposes. Additionally, if your submission is successful, the point of contact for the submission should also receive an email from NCBI notifying them of their submission success.
+
+
| Variable | Description | Type |
| --- | --- | --- |
| biosample_failures | Text file listing samples that failed BioSample submission | File |
@@ -193,6 +199,8 @@ The output files contain information mostly for debugging purposes. Additionally
| terra_2_ncbi_analysis_date | Date that the workflow was run | String |
| terra_2_ncbi_version | Version of the PHB repository where the workflow is hosted | String |
+
+
???+ toggle "An example excluded_samples.tsv file"
##### An example excluded_samples.tsv file {#example-excluded-samples}
diff --git a/docs/workflows/standalone/gambit_query.md b/docs/workflows/standalone/gambit_query.md
index 5d6dd3c44..095b6e463 100644
--- a/docs/workflows/standalone/gambit_query.md
+++ b/docs/workflows/standalone/gambit_query.md
@@ -12,6 +12,8 @@ The GAMBIT_Query_PHB workflow performs taxon assignment of a genome assembly usi
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| gambit_query | **assembly_fasta** | File | Assembly file in FASTA format | | Required |
@@ -23,6 +25,8 @@ The GAMBIT_Query_PHB workflow performs taxon assignment of a genome assembly usi
| gambit | **gambit_db_genomes** | File | Database of metadata for assembled query genomes; requires complementary signatures file. If not provided, uses default database "/gambit-db" | "gs://gambit-databases-rp/2.0.0/gambit-metadata-2.0.0-20240628.gdb" | Optional |
| gambit | **gambit_db_signatures** | File | Signatures file; requires complementary genomes file. If not specified, the file from the docker container will be used. | "gs://gambit-databases-rp/2.0.0/gambit-signatures-2.0.0-20240628.gs" | Optional |
+
+
### Workflow Tasks
[`GAMBIT`](https://github.com/jlumpe/gambit) determines the taxon of the genome assembly using a k-mer based approach to match the assembly sequence to the closest complete genome in a database, thereby predicting its identity. Sometimes, GAMBIT can confidently designate the organism to the species level. Other times, it is more conservative and assigns it to a higher taxonomic rank.
@@ -40,6 +44,8 @@ For additional details regarding the GAMBIT tool and a list of available GAMBIT
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| gambit_closest_genomes | File | CSV file listing genomes in the GAMBIT database that are most similar to the query assembly |
@@ -50,6 +56,8 @@ For additional details regarding the GAMBIT tool and a list of available GAMBIT
| gambit_query_wf_analysis_date | String | Date of analysis |
| gambit_query_wf_version | String | PHB repository version |
| gambit_report | File | GAMBIT report in a machine-readable format |
-| gambit_version | String | Version of gambit software used
+| gambit_version | String | Version of gambit software used |
+
+
> GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. Lumpe et al. PLOS ONE, 2022. DOI: [10.1371/journal.pone.0277575](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0277575)
diff --git a/docs/workflows/standalone/kraken2.md b/docs/workflows/standalone/kraken2.md
index ffef97db3..df36e56a1 100644
--- a/docs/workflows/standalone/kraken2.md
+++ b/docs/workflows/standalone/kraken2.md
@@ -30,6 +30,8 @@ Besides the data input types, there are minimal differences between these two wo
#### Suggested databases
+
+
| 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 |
@@ -40,8 +42,12 @@ Besides the data input types, there are minimal differences between these two wo
| **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 |
+
+
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | **Workflow** |
|---|---|---|---|---|---|---|
| *workflow_name | **kraken2_db** | File | A Kraken2 database in .tar.gz format | | Required | ONT, PE, SE |
@@ -67,8 +73,12 @@ Besides the data input types, there are minimal differences between these two wo
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional | ONT, PE, SE |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional | ONT, PE, SE |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| kraken2_classified_read1 | File | FASTQ file of classified forward/R1 reads |
@@ -85,6 +95,8 @@ Besides the data input types, there are minimal differences between these two wo
| krona_html | File | HTML report of krona with visualisation of taxonomic classification of reads (if PE or SE) |
| krona_version | String | krona version (if PE or SE) |
+
+
#### Interpretation of results
The most important outputs of the Kraken2 workflows are the `kraken2_report` files. These will include a breakdown of the number of sequences assigned to a particular taxon, and the percentage of reads assigned. [A complete description of the report format can be found here](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#standard-kraken-output-format).
diff --git a/docs/workflows/standalone/ncbi_amrfinderplus.md b/docs/workflows/standalone/ncbi_amrfinderplus.md
index 237e79039..38def0e99 100644
--- a/docs/workflows/standalone/ncbi_amrfinderplus.md
+++ b/docs/workflows/standalone/ncbi_amrfinderplus.md
@@ -19,6 +19,8 @@ You can check if a gene or point mutation is in the AMRFinderPlus database [here
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| amrfinderplus_wf | **assembly** | File | Genome assembly file in FASTA format. Can be generated by TheiaProk workflow or other bioinformatics workflows. | | Required |
@@ -35,8 +37,12 @@ You can check if a gene or point mutation is in the AMRFinderPlus database [here
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| amrfinderplus_all_report | File | Output TSV file from AMRFinderPlus (described [here](https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus#fields)) |
@@ -54,6 +60,8 @@ You can check if a gene or point mutation is in the AMRFinderPlus database [here
| amrfinderplus_wf_analysis_date | String | Date of analysis |
| amrfinderplus_wf_version | String | Version of PHB used for the analysis |
+
+
## References
>Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021 Jun 16;11(1):12728. doi: 10.1038/s41598-021-91456-0. PMID: 34135355; PMCID: PMC8208984.
diff --git a/docs/workflows/standalone/ncbi_scrub.md b/docs/workflows/standalone/ncbi_scrub.md
index e5e4bd6eb..0ae60c49b 100644
--- a/docs/workflows/standalone/ncbi_scrub.md
+++ b/docs/workflows/standalone/ncbi_scrub.md
@@ -16,6 +16,8 @@ There are three Kraken2 workflows:
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | **Workflow** |
|---|---|---|---|---|---|---|
| dehost_pe or dehost_se | **read1** | File | | | Required | PE, SE |
@@ -35,6 +37,8 @@ There are three Kraken2 workflows:
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional | PE, SE |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional | PE, SE |
+
+
### Workflow Tasks
This workflow is composed of two tasks, one to dehost the input reads and another to screen the clean reads with kraken2 and the viral+human database.
@@ -69,6 +73,8 @@ This workflow is composed of two tasks, one to dehost the input reads and anothe
### Outputs
+
+
| **Variable** | **Type** | **Description** | **Workflow** |
|---|---|---|---|
| kraken_human_dehosted | Float | Percent of human read data detected using the Kraken2 software after host removal | PE, SE |
@@ -82,3 +88,4 @@ This workflow is composed of two tasks, one to dehost the input reads and anothe
| read1_dehosted | File | Dehosted forward reads | PE, SE |
| read2_dehosted | File | Dehosted reverse reads | PE |
+
\ No newline at end of file
diff --git a/docs/workflows/standalone/rasusa.md b/docs/workflows/standalone/rasusa.md
index 055b235f5..38052ff41 100644
--- a/docs/workflows/standalone/rasusa.md
+++ b/docs/workflows/standalone/rasusa.md
@@ -27,6 +27,8 @@ RASUSA functions to randomly downsample the number of raw reads to a user-define
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Attribute** | **Terra Status** |
|---|---|---|---|---|---|
| rasusa_workflow | **coverage** | Float | Use to specify the desired coverage of reads after downsampling; actual coverage of subsampled reads will not be exact and may be slightly higher; always check the estimated clean coverage after performing downstream workflows to verify coverage values, when necessary | | Required |
@@ -45,8 +47,12 @@ RASUSA functions to randomly downsample the number of raw reads to a user-define
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| rasusa_version | String | Version of RASUSA used for the analysis |
@@ -55,6 +61,8 @@ RASUSA functions to randomly downsample the number of raw reads to a user-define
| read1_subsampled | File | New read1 FASTQ files downsampled to desired coverage |
| read2_subsampled | File | New read2 FASTQ files downsampled to desired coverage |
+
+
!!! tip "Don't Forget!"
Remember to use the subsampled reads in downstream analyses with `this.read1_subsampled` and `this.read2_subsampled` inputs.
diff --git a/docs/workflows/standalone/rename_fastq.md b/docs/workflows/standalone/rename_fastq.md
index 19ec4b4a6..d8d7196ba 100644
--- a/docs/workflows/standalone/rename_fastq.md
+++ b/docs/workflows/standalone/rename_fastq.md
@@ -12,6 +12,8 @@ This sample-level workflow receives a read file or a pair of read files (FASTQ),
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| rename_fastq_files | **new_filename** | String | New name for the FASTQ file(s) | | Required |
@@ -24,6 +26,8 @@ This sample-level workflow receives a read file or a pair of read files (FASTQ),
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Outputs
If a reverse read (`read2`) is provided, the files get renamed to the provided `new_filename` input with the notation `_R1.fastq.gz` and `_R2.fastq.gz`. If only `read1` is provided, the file is renamed to `.fastq.gz`.
diff --git a/docs/workflows/standalone/tbprofiler_tngs.md b/docs/workflows/standalone/tbprofiler_tngs.md
index 3e505cabb..d0061fdd7 100644
--- a/docs/workflows/standalone/tbprofiler_tngs.md
+++ b/docs/workflows/standalone/tbprofiler_tngs.md
@@ -12,6 +12,8 @@ This workflow is still in experimental research stages. Documentation is minimal
### Inputs
+
+
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
|---|---|---|---|---|---|
| tbprofiler_tngs | **read1** | File | Illumina forward read file in FASTQ file format (compression optional) | | Required |
@@ -62,8 +64,12 @@ This workflow is still in experimental research stages. Documentation is minimal
| version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
| version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | | Optional |
+
+
### Terra Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| tbp_parser_average_genome_depth | Float | The mean depth of coverage across all target regions included in the analysis |
@@ -95,3 +101,5 @@ This workflow is still in experimental research stages. Documentation is minimal
| trimmomatic_read2_trimmed | File | The read2 file post trimming |
| trimmomatic_stats | File | The read trimming statistics |
| trimmomatic_version | String | The version of trimmomatic used in this analysis |
+
+
diff --git a/docs/workflows/standalone/theiavalidate.md b/docs/workflows/standalone/theiavalidate.md
index 2dfd5b2b6..a9c051f9c 100644
--- a/docs/workflows/standalone/theiavalidate.md
+++ b/docs/workflows/standalone/theiavalidate.md
@@ -39,6 +39,8 @@ If a column consists of only GCP URIs (Google Cloud file paths), the files will
### Inputs
+
+
Please note that all string inputs **must** be enclosed in quotation marks; for example, "column1,column2" or "workspace1"
| **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
@@ -62,6 +64,8 @@ Please note that all string inputs **must** be enclosed in quotation marks; for
| export_two_tsvs | **cpu** | Int | Number of CPUs to allocate to the task | 1 | Optional |
| export_two_tsvs | **disk_size** | Int | Amount of storage (in GB) to allocate to the task | 10 | Optional |
+
+
The optional `validation_criteria_tsv` file takes the following format (tab-delimited; _a header line is required_):
```text linenums="1"
@@ -95,6 +99,8 @@ Please note that the name in the **second column** will be displayed and used in
### Outputs
+
+
| **Variable** | **Type** | **Description** |
|---|---|---|
| theiavalidate_criteria_differences | File | A TSV file that lists only the differences that fail to meet the validation criteria |
@@ -108,6 +114,8 @@ Please note that the name in the **second column** will be displayed and used in
| theiavalidate_version | String | The version of the TheiaValidate Python Docker |
| theiavalidate_wf_version | String | The version of the PHB repository |
+
+
### Example Data and Outputs
To help demonstrate how TheiaValidate works, please observe the following example and outputs:
diff --git a/docs/workflows_overview/workflows_alphabetically.md b/docs/workflows_overview/workflows_alphabetically.md
index 128e9bee7..5195dc0f5 100644
--- a/docs/workflows_overview/workflows_alphabetically.md
+++ b/docs/workflows_overview/workflows_alphabetically.md
@@ -6,6 +6,8 @@ title: Alphabetical Workflows
---
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Assembly_Fetch**](../workflows/data_import/assembly_fetch.md) | Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly | Any taxa | Sample-level | Yes | v1.3.0 | [Assembly_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Assembly_Fetch_PHB:main?tab=info) |
@@ -49,6 +51,8 @@ title: Alphabetical Workflows
| [**Usher_PHB**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v1.2.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_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) |
+
+
*[Sample-level]: This workflow is run once for each sample
*[Set-level]: This workflow is run once on a group of samples
diff --git a/docs/workflows_overview/workflows_kingdom.md b/docs/workflows_overview/workflows_kingdom.md
index ab8575a64..c9c001ec6 100644
--- a/docs/workflows_overview/workflows_kingdom.md
+++ b/docs/workflows_overview/workflows_kingdom.md
@@ -8,6 +8,7 @@ title: Workflows by Kingdom
### Any Taxa
+
| **Name** | **Description** | **Taxa** | **Workflow Level** | **Command-line Compatible**[^1] | **Last known changes** | **Dockstore** |
|---|---|---|---|---|---|---|
@@ -25,8 +26,12 @@ title: Workflows by Kingdom
| [**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) |
+
+
### Bacteria
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Core_Gene_SNP**](../workflows/phylogenetic_construction/core_gene_snp.md) | Pangenome analysis | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Core_Gene_SNP_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Core_Gene_SNP_PHB:main?tab=info) |
@@ -44,8 +49,12 @@ title: Workflows by Kingdom
| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_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 | v2.2.0 | [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) |
+
+
### Mycotics
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Cauris_CladeTyper**](../workflows/standalone/cauris_cladetyper.md)| C. auris clade assignment | Mycotics | Sample-level | Yes | v1.0.0 | [Cauris_CladeTyper_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Cauris_CladeTyper_PHB:main?tab=info) |
@@ -58,8 +67,11 @@ title: Workflows by Kingdom
| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_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 | v2.0.1 | [TheiaEuk_Illumina_PE_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TheiaEuk_Illumina_PE_PHB:main?tab=info) |
+
+
### Viral
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
@@ -79,6 +91,8 @@ title: Workflows by Kingdom
| [**Usher_PHB**](../workflows/phylogenetic_placement/usher.md)| Use UShER to rapidly and accurately place your samples on any existing phylogenetic tree | Monkeypox virus, SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.1.0 | [Usher_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Usher_PHB:main?tab=info) |
| [**VADR_Update**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v1.2.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
+
+
*[Sample-level]: This workflow is run once for each sample
*[Set-level]: This workflow is run once on a group of samples
diff --git a/docs/workflows_overview/workflows_type.md b/docs/workflows_overview/workflows_type.md
index 5e7e024b6..375c73e71 100644
--- a/docs/workflows_overview/workflows_type.md
+++ b/docs/workflows_overview/workflows_type.md
@@ -8,6 +8,8 @@ title: Workflows by Type
### Data Import
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Assembly_Fetch**](../workflows/data_import/assembly_fetch.md) | Download assemblies from NCBI, after optionally identifying the closest RefSeq reference genome to your own draft assembly | Any taxa | Sample-level | Yes | v1.3.0 | [Assembly_Fetch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Assembly_Fetch_PHB:main?tab=info) |
@@ -15,8 +17,12 @@ title: Workflows by Type
| [**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) |
| [**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) |
+
+
### Genomic Characterization
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**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) |
@@ -28,8 +34,12 @@ title: Workflows by Type
| [**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 | v2.2.0 | [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) |
| [**VADR_Update**](../workflows/genomic_characterization/vadr_update.md)| Update VADR assignments | HAV, Influenza, Monkeypox virus, RSV-A, RSV-B, SARS-CoV-2, Viral, WNV | Sample-level | Yes | v1.2.1 | [VADR_Update_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/VADR_Update_PHB:main?tab=info) |
+
+
### Phylogenetic Construction
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Augur**](../workflows/phylogenetic_construction/augur.md) | Phylogenetic analysis for viral pathogens | Viral | Sample-level, Set-level | Yes | v2.1.0 | [Augur_Prep_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_Prep_PHB:main?tab=info), [Augur_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Augur_PHB:main?tab=info) |
@@ -44,31 +54,47 @@ title: Workflows by Type
| [**Snippy_Tree**](../workflows/phylogenetic_construction/snippy_tree.md)| SNP-based phylogenetic analysis from reads, with option to mask recombination | Bacteria | Set-level | Some optional features incompatible, Yes | v2.1.0 | [Snippy_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Tree_PHB:main?tab=info) |
| [**Snippy_Variants**](../workflows/phylogenetic_construction/snippy_variants.md)| Alignment of reads to a reference genome, then SNP calling | Bacteria, Mycotics, Viral | Sample-level | Yes | v2.2.0 | [Snippy_Variants_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Snippy_Variants_PHB:main?tab=info) |
+
+
### Phylogenetic Placement
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Samples_to_Ref_Tree**](../workflows/phylogenetic_placement/samples_to_ref_tree.md)| Use Nextclade to rapidly and accurately place your samples on any existing phylogenetic tree | Monkeypox virus, SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.1.0 | [Samples_to_Ref_Tree_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Samples_to_Ref_Tree_PHB:main?tab=info) |
| [**Usher_PHB**](../workflows/phylogenetic_placement/usher.md)| Use UShER to rapidly and accurately place your samples on any existing phylogenetic tree | Monkeypox virus, SARS-CoV-2, Viral | Sample-level, Set-level | Yes | v2.1.0 | [Usher_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Usher_PHB:main?tab=info) |
+
+
### Public Data Sharing
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Mercury_Prep_N_Batch**](../workflows/public_data_sharing/mercury_prep_n_batch.md)| Prepare metadata and sequence data for submission to NCBI and GISAID | Influenza, Monkeypox virus, SARS-CoV-2, Viral | Set-level | No | v2.2.0 | [Mercury_Prep_N_Batch_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Mercury_Prep_N_Batch_PHB:main?tab=info) |
| [**Terra_2_GISAID**](../workflows/public_data_sharing/terra_2_gisaid.md)| Upload of assembly data to GISAID | SARS-CoV-2, Viral | Set-level | Yes | v1.2.1 | [Terra_2_GISAID_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_GISAID_PHB:main?tab=info) |
| [**Terra_2_NCBI**](../workflows/public_data_sharing/terra_2_ncbi.md)| Upload of sequence data to NCBI | Bacteria, Mycotics, Viral | Set-level | No | v2.1.0 | [Terra_2_NCBI_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Terra_2_NCBI_PHB:main?tab=info) |
+
+
### Exporting Data from Terra
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Concatenate_Column_Content**](../workflows/data_export/concatenate_column_content.md) | Concatenate contents of a specified Terra data table column for many samples ("entities") | Any taxa | Set-level | Yes | v2.1.0 | [Concatenate_Column_Content_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Concatenate_Column_Content_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) |
+
+
### Standalone
+
+
| **Name** | **Description** | **Applicable Kingdom** | **Workflow Level** | **Command-line Compatibility**[^1] | **Last Known Changes** | **Dockstore** |
|---|---|---|---|---|---|---|
| [**Cauris_CladeTyper**](../workflows/standalone/cauris_cladetyper.md)| C. auris clade assignment | Mycotics | Sample-level | Yes | v1.0.0 | [Cauris_CladeTyper_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/Cauris_CladeTyper_PHB:main?tab=info) |
@@ -81,6 +107,8 @@ title: Workflows by Type
| [**TBProfiler_tNGS**](../workflows/standalone/tbprofiler_tngs.md)| Performs in silico antimicrobial susceptibility testing on Mycobacterium tuberculosis targeted-NGS samples with TBProfiler and tbp-parser | Bacteria, TB | Sample-level | Yes | v2.0.0 | [TBProfiler_tNGS_PHB](https://dockstore.org/workflows/github.com/theiagen/public_health_bioinformatics/TBProfiler_tNGS_PHB:smw-tngs-tbprofiler-dev?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) |
+
+
*[Sample-level]: This workflow is run once for each sample
*[Set-level]: This workflow is run once on a group of samples
diff --git a/mkdocs.yml b/mkdocs.yml
index fbe6df019..6c35901bc 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -23,7 +23,7 @@ nav:
- Freyja Workflow Series: workflows/genomic_characterization/freyja.md
- Pangolin_Update: workflows/genomic_characterization/pangolin_update.md
- TheiaCoV Workflow Series: workflows/genomic_characterization/theiacov.md
- - TheiaEuk: workflows/genomic_characterization/theiaeuk.md
+ - TheiaEuk Workflow Series: workflows/genomic_characterization/theiaeuk.md
- TheiaMeta: workflows/genomic_characterization/theiameta.md
- TheiaMeta_Panel: workflows/genomic_characterization/theiameta_panel.md
- TheiaProk Workflow Series: workflows/genomic_characterization/theiaprok.md
@@ -101,7 +101,7 @@ nav:
- NCBI-AMRFinderPlus: workflows/standalone/ncbi_amrfinderplus.md
- Snippy_Variants: workflows/phylogenetic_construction/snippy_variants.md
- Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md
- - TheiaEuk: workflows/genomic_characterization/theiaeuk.md
+ - TheiaEuk Workflow Series: workflows/genomic_characterization/theiaeuk.md
- Viral:
- Augur: workflows/phylogenetic_construction/augur.md
- CZGenEpi_Prep: workflows/phylogenetic_construction/czgenepi_prep.md
@@ -151,7 +151,7 @@ nav:
- Terra_2_GISAID: workflows/public_data_sharing/terra_2_gisaid.md
- Terra_2_NCBI: workflows/public_data_sharing/terra_2_ncbi.md
- TheiaCoV Workflow Series: workflows/genomic_characterization/theiacov.md
- - TheiaEuk: workflows/genomic_characterization/theiaeuk.md
+ - TheiaEuk Workflow Series: workflows/genomic_characterization/theiaeuk.md
- TheiaMeta: workflows/genomic_characterization/theiameta.md
- TheiaMeta_Panel: workflows/genomic_characterization/theiameta_panel.md
- TheiaProk Workflow Series: workflows/genomic_characterization/theiaprok.md
@@ -233,11 +233,12 @@ plugins:
# - section-index
extra_javascript:
- - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
- - javascripts/tablesort.js
+ - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
+ - javascripts/tablesort.js
+ - javascripts/table-search.js
extra_css:
- - stylesheets/extra.css
+ - stylesheets/extra.css
extra:
social:
@@ -254,4 +255,4 @@ extra:
homepage: https://www.theiagen.com
copyright: |
- © 2022-2024 Theiagen Genomics
\ No newline at end of file
+ © 2022-2024 Theiagen Genomics
diff --git a/tasks/assembly/task_artic_consensus.wdl b/tasks/assembly/task_artic_consensus.wdl
index 6e38334a1..8e2d174db 100644
--- a/tasks/assembly/task_artic_consensus.wdl
+++ b/tasks/assembly/task_artic_consensus.wdl
@@ -12,7 +12,7 @@ task consensus {
Int memory = 16
Int disk_size = 100
String medaka_model = "r941_min_high_g360"
- String docker = "us-docker.pkg.dev/general-theiagen/staphb/artic-ncov2019-epi2me"
+ String docker = "us-docker.pkg.dev/general-theiagen/staphb/artic:1.2.4-1.12.0"
}
String primer_name = basename(primer_bed)
command <<<
@@ -61,7 +61,13 @@ task consensus {
# version control
echo "Medaka via $(artic -v)" | tee VERSION
echo "~{primer_name}" | tee PRIMER_NAME
- artic minion --medaka --medaka-model ~{medaka_model} --normalise ~{normalise} --threads ~{cpu} --scheme-directory ./primer-schemes --read-file ~{read1} ${scheme_name} ~{samplename}
+ artic minion \
+ --medaka \
+ --medaka-model ~{medaka_model} \
+ --normalise ~{normalise} \
+ --threads ~{cpu} \
+ --scheme-directory ./primer-schemes \
+ --read-file ~{read1} ${scheme_name} ~{samplename}
gunzip -f ~{samplename}.pass.vcf.gz
# clean up fasta header
diff --git a/tasks/quality_control/comparisons/task_screen.wdl b/tasks/quality_control/comparisons/task_screen.wdl
index 8cc6f58e0..3934d0b7a 100644
--- a/tasks/quality_control/comparisons/task_screen.wdl
+++ b/tasks/quality_control/comparisons/task_screen.wdl
@@ -20,6 +20,9 @@ task check_reads {
Int cpu = 1
}
command <<<
+ # just in case anything fails, throw an error
+ set -euo pipefail
+
flag="PASS"
# initalize estimated genome length
@@ -34,13 +37,13 @@ task check_reads {
fi
# check one: number of reads
- read1_num=`eval "$cat_reads ~{read1}" | awk '{s++}END{print s/4}'`
- read2_num=`eval "$cat_reads ~{read2}" | awk '{s++}END{print s/4}'`
- # awk '{s++}END{print s/4' counts the number of lines and divides them by 4
- # key assumption: in fastq there will be four lines per read
- # sometimes fastqs do not have 4 lines per read, so this might fail one day
+ read1_num=$($cat_reads ~{read1} | fastq-scan | grep 'read_total' | sed 's/[^0-9]*\([0-9]\+\).*/\1/')
+ read2_num=$($cat_reads ~{read2} | fastq-scan | grep 'read_total' | sed 's/[^0-9]*\([0-9]\+\).*/\1/')
+ echo "DEBUG: Number of reads in R1: ${read1_num}"
+ echo "DEBUG: Number of reads in R2: ${read2_num}"
reads_total=$(expr $read1_num + $read2_num)
+ echo "DEBUG: Number of reads total in R1 and R2: ${reads_total}"
if [ "${reads_total}" -le "~{min_reads}" ]; then
flag="FAIL; the total number of reads is below the minimum of ~{min_reads}"
@@ -51,13 +54,11 @@ task check_reads {
# checks two and three: number of basepairs and proportion of sequence
if [ "${flag}" == "PASS" ]; then
# count number of basepairs
- # this only works if the fastq has 4 lines per read, so this might fail one day
- read1_bp=`eval "${cat_reads} ~{read1}" | paste - - - - | cut -f2 | tr -d '\n' | wc -c`
- read2_bp=`eval "${cat_reads} ~{read2}" | paste - - - - | cut -f2 | tr -d '\n' | wc -c`
- # paste - - - - (print 4 consecutive lines in one row, tab delimited)
- # cut -f2 print only the second column (the second line of the fastq 4-line)
- # tr -d '\n' removes line endings
- # wc -c counts characters
+ # using fastq-scan to count the number of basepairs in each fastq
+ read1_bp=$(eval "${cat_reads} ~{read1}" | fastq-scan | grep 'total_bp' | sed 's/[^0-9]*\([0-9]\+\).*/\1/')
+ read2_bp=$(eval "${cat_reads} ~{read2}" | fastq-scan | grep 'total_bp' | sed 's/[^0-9]*\([0-9]\+\).*/\1/')
+ echo "DEBUG: Number of basepairs in R1: $read1_bp"
+ echo "DEBUG: Number of basepairs in R2: $read2_bp"
# set proportion variables for easy comparison
# removing the , 2) to make these integers instead of floats
@@ -147,7 +148,8 @@ task check_reads {
flag="FAIL; the estimated coverage (${estimated_coverage}) is less than the minimum of ~{min_coverage}x"
else
flag="PASS"
- echo $estimated_genome_length | tee EST_GENOME_LENGTH
+ echo ${estimated_genome_length} | tee EST_GENOME_LENGTH
+ echo "DEBUG: estimated_genome_length: ${estimated_genome_length}"
fi
fi
fi
@@ -190,6 +192,9 @@ task check_reads_se {
Int cpu = 1
}
command <<<
+ # just in case anything fails, throw an error
+ set -euo pipefail
+
flag="PASS"
# initalize estimated genome length
@@ -203,11 +208,9 @@ task check_reads_se {
cat_reads="cat"
fi
- # check one: number of reads
- read1_num=`eval "$cat_reads ~{read1}" | awk '{s++}END{print s/4}'`
- # awk '{s++}END{print s/4' counts the number of lines and divides them by 4
- # key assumption: in fastq there will be four lines per read
- # sometimes fastqs do not have 4 lines per read, so this might fail one day
+ # check one: number of reads via fastq-scan
+ read1_num=$($cat_reads ~{read1} | fastq-scan | grep 'read_total' | sed 's/[^0-9]*\([0-9]\+\).*/\1/')
+ echo "DEBUG: Number of reads in R1: ${read1_num}"
if [ "${read1_num}" -le "~{min_reads}" ] ; then
flag="FAIL; the number of reads (${read1_num}) is below the minimum of ~{min_reads}"
@@ -218,12 +221,9 @@ task check_reads_se {
# checks two and three: number of basepairs and proportion of sequence
if [ "${flag}" == "PASS" ]; then
# count number of basepairs
- # this only works if the fastq has 4 lines per read, so this might fail one day
- read1_bp=`eval "${cat_reads} ~{read1}" | paste - - - - | cut -f2 | tr -d '\n' | wc -c`
- # paste - - - - (print 4 consecutive lines in one row, tab delimited)
- # cut -f2 print only the second column (the second line of the fastq 4-line)
- # tr -d '\n' removes line endings
- # wc -c counts characters
+ # using fastq-scan to count the number of basepairs in each fastq
+ read1_bp=$(eval "${cat_reads} ~{read1}" | fastq-scan | grep 'total_bp' | sed 's/[^0-9]*\([0-9]\+\).*/\1/')
+ echo "DEBUG: Number of basepairs in R1: $read1_bp"
if [ "$flag" == "PASS" ] ; then
if [ "${read1_bp}" -le "~{min_basepairs}" ] ; then
@@ -309,7 +309,8 @@ task check_reads_se {
fi
echo $flag | tee FLAG
- echo $estimated_genome_length | tee EST_GENOME_LENGTH
+ echo ${estimated_genome_length} | tee EST_GENOME_LENGTH
+ echo "DEBUG: estimated_genome_length: ${estimated_genome_length}"
>>>
output {
String read_screen = read_string("FLAG")
diff --git a/tasks/utilities/submission/task_mercury.wdl b/tasks/utilities/submission/task_mercury.wdl
index 51ce839e1..d445e92aa 100644
--- a/tasks/utilities/submission/task_mercury.wdl
+++ b/tasks/utilities/submission/task_mercury.wdl
@@ -29,6 +29,9 @@ task mercury {
volatile: true
}
command <<<
+ #set -euo pipefail to avoid silent failure
+ set -euo pipefail
+
python3 /mercury/mercury/mercury.py -v | tee VERSION
python3 /mercury/mercury/mercury.py \
diff --git a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
index 48ffe30c9..599fec45e 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml
@@ -17,7 +17,7 @@
- wf_theiacov_clearlabs_miniwdl
files:
- path: miniwdl_run/call-consensus/command
- md5sum: a8e200703dedf732b45dd92b0af15f1c
+ md5sum: b19d5ce485c612036064c07f0a1d6a18
- path: miniwdl_run/call-consensus/inputs.json
contains: ["read1", "samplename", "fastq"]
- path: miniwdl_run/call-consensus/outputs.json
diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
index b1bb6da13..4c7542334 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml
@@ -138,7 +138,7 @@
md5sum: 7c5aba41f53293b712fd86d08ed5b36e
# clean read screen
- path: miniwdl_run/call-clean_check_reads/command
- md5sum: e18830c68993b2837d1da29ce55d2de8
+ md5sum: aeeb107f328ccd7d2d805dc5990b24ac
- path: miniwdl_run/call-clean_check_reads/inputs.json
contains: ["read1", "read2", "organism"]
- path: miniwdl_run/call-clean_check_reads/outputs.json
diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
index 9af5b61c9..0742c19a9 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml
@@ -94,7 +94,7 @@
md5sum: 9a089b8920e55c9cc7bc8cd7d18f9a8e
# clean read screen
- path: miniwdl_run/call-clean_check_reads/command
- md5sum: aec6c57452ddff84c325601a780605d2
+ md5sum: 80a361915a627e86743baacfc383b2b5
- path: miniwdl_run/call-clean_check_reads/inputs.json
contains: ["read1", "organism"]
- path: miniwdl_run/call-clean_check_reads/outputs.json
diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml
index 1772e16b4..6077323b9 100644
--- a/tests/workflows/theiacov/test_wf_theiacov_ont.yml
+++ b/tests/workflows/theiacov/test_wf_theiacov_ont.yml
@@ -17,7 +17,7 @@
- wf_theiacov_ont_miniwdl
files:
- path: miniwdl_run/call-clean_check_reads/command
- md5sum: 2517c5cf87db0af66663ffb5e69f6b4f
+ md5sum: 8078e96573428b712ddcb06517333cf5
- path: miniwdl_run/call-clean_check_reads/inputs.json
- path: miniwdl_run/call-clean_check_reads/outputs.json
- path: miniwdl_run/call-clean_check_reads/stderr.txt
@@ -31,7 +31,7 @@
- path: miniwdl_run/call-clean_check_reads/work/_miniwdl_inputs/0/artic_ncov2019_ont.fastq
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: miniwdl_run/call-consensus/command
- md5sum: 056563d18294928fef5238bac7213791
+ md5sum: 362dccda19ecadf377d5cd5872946ddd
- path: miniwdl_run/call-consensus/inputs.json
contains: ["read1_clean", "samplename", "fastq"]
- path: miniwdl_run/call-consensus/outputs.json
@@ -45,7 +45,7 @@
- path: miniwdl_run/call-consensus/work/REFERENCE_GENOME
md5sum: 0e6efd549c8773f9a2f7a3e82619ee61
- path: miniwdl_run/call-consensus/work/VERSION
- md5sum: f3528ff85409c70100063c55ad75612b
+ md5sum: 394e07bc6788e025ac35254411db107c
- path: miniwdl_run/call-consensus/work/_miniwdl_inputs/0/artic-v3.primers.bed
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: miniwdl_run/call-consensus/work/_miniwdl_inputs/0/artic_ncov2019_ont.fastq
@@ -64,8 +64,6 @@
- path: miniwdl_run/call-consensus/work/ont.fastq.gz
- path: miniwdl_run/call-consensus/work/ont.medaka.consensus.fasta
md5sum: d36b7c665aa4127f0a6e8dbc562eea3e
- - path: miniwdl_run/call-consensus/work/ont.merged.gvcf.vcf.gz
- - path: miniwdl_run/call-consensus/work/ont.merged.gvcf.vcf.gz.tbi
- path: miniwdl_run/call-consensus/work/ont.merged.vcf.gz
- path: miniwdl_run/call-consensus/work/ont.merged.vcf.gz.tbi
- path: miniwdl_run/call-consensus/work/ont.minion.log.txt
@@ -73,20 +71,15 @@
- path: miniwdl_run/call-consensus/work/ont.pass.vcf.gz.tbi
- path: miniwdl_run/call-consensus/work/ont.preconsensus.fasta
md5sum: b68f4ee4abc9fc16215204d0ff754bb8
- - path: miniwdl_run/call-consensus/work/ont.preconsensus.fasta.fai
- md5sum: 4ca7d9fd06b9cdf379c2cf02b9fd6d0e
- path: miniwdl_run/call-consensus/work/ont.primers.vcf
- path: miniwdl_run/call-consensus/work/ont.primersitereport.txt
- md5sum: cffee67632a262eeb947cea9cee0b4c1
+ md5sum: dab514423a8fb7b59ab7870ad8c3b4cf
- path: miniwdl_run/call-consensus/work/ont.primertrimmed.rg.sorted.bam
- path: miniwdl_run/call-consensus/work/ont.primertrimmed.rg.sorted.bam.bai
- path: miniwdl_run/call-consensus/work/ont.sorted.bam
- path: miniwdl_run/call-consensus/work/ont.sorted.bam.bai
- path: miniwdl_run/call-consensus/work/ont.trimmed.rg.sorted.bam
- path: miniwdl_run/call-consensus/work/ont.trimmed.rg.sorted.bam.bai
- - path: miniwdl_run/call-consensus/work/ont.vcfcheck.log
- - path: miniwdl_run/call-consensus/work/ont.vcfreport.txt
- md5sum: 69131186223267b3ae6621cb8ef4eecd
- path: miniwdl_run/call-consensus/work/primer-schemes/SARS-CoV-2/Vuser/SARS-CoV-2.reference.fasta
md5sum: b9b67235a2d9d0b0d7f531166ffefd41
- path: miniwdl_run/call-consensus/work/primer-schemes/SARS-CoV-2/Vuser/SARS-CoV-2.reference.fasta.fai
@@ -219,7 +212,7 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: miniwdl_run/call-pangolin4/work/ont.pangolin_report.csv
- path: miniwdl_run/call-raw_check_reads/command
- md5sum: 1858d98f3c15904be0c219b867727048
+ md5sum: 5df9a70c852960f82c84c7da611cd177
- path: miniwdl_run/call-raw_check_reads/inputs.json
- path: miniwdl_run/call-raw_check_reads/outputs.json
- path: miniwdl_run/call-raw_check_reads/stderr.txt
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
index d2cedb29b..91ae801b7 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
@@ -201,7 +201,7 @@
- path: miniwdl_run/call-cg_pipeline_raw/work/test_readMetrics.tsv
contains: ["File", "fastq", "coverage"]
- path: miniwdl_run/call-clean_check_reads/command
- md5sum: 8235bc815fe3b57471f97474bff3e3f7
+ md5sum: f28c2b4597398988bc9016505425f6f0
- path: miniwdl_run/call-clean_check_reads/inputs.json
contains: ["read1", "fastq", "skip_screen", "true"]
- path: miniwdl_run/call-clean_check_reads/outputs.json
@@ -364,7 +364,7 @@
- path: miniwdl_run/call-quast/work/transposed_report.txt
contains: ["Assembly", "length", "contigs", "test"]
- path: miniwdl_run/call-raw_check_reads/command
- md5sum: fd8c392c24e4e49859bdd006163db646
+ md5sum: 0e417649675499e2be549ce82e02704c
- path: miniwdl_run/call-raw_check_reads/inputs.json
contains: ["read1", "fastq", "skip_screen", "true"]
- path: miniwdl_run/call-raw_check_reads/outputs.json
@@ -581,7 +581,7 @@
- path: miniwdl_run/wdl/tasks/quality_control/basic_statistics/task_quast.wdl
contains: ["version", "quast", "output"]
- path: miniwdl_run/wdl/tasks/quality_control/comparisons/task_screen.wdl
- md5sum: 75631c4db89792a939e4d872adc05b86
+ md5sum: adb43c5bf0a83b9e2ef7669ed2d1760f
- path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_trimmomatic.wdl
contains: ["version", "trimmomatic", "output"]
- path: miniwdl_run/wdl/tasks/species_typing/escherichia_shigella/task_ectyper.wdl
@@ -633,7 +633,7 @@
- path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl
md5sum: 6d9dd969e2144ca23f2a0e101e6b6966
- path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
- md5sum: 8ab95440118d06dd3c07765a19e876e7
+ md5sum: 670f990128063eb3c7b3fa49302f08b7
- path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl
contains: ["version", "QC", "output"]
- path: miniwdl_run/workflow.log
diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
index d19f1319e..82f9a9a74 100644
--- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
+++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
@@ -194,7 +194,7 @@
- path: miniwdl_run/call-cg_pipeline_raw/work/test_readMetrics.tsv
contains: ["File", "fastq", "coverage"]
- path: miniwdl_run/call-clean_check_reads/command
- md5sum: 1ed4ae1859ade5045c01c92dfe54899c
+ md5sum: 51f799af8609c440d51e0046ebc030e8
- path: miniwdl_run/call-clean_check_reads/inputs.json
contains: ["read1", "fastq", "skip_screen", "true"]
- path: miniwdl_run/call-clean_check_reads/outputs.json
@@ -203,7 +203,7 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: miniwdl_run/call-clean_check_reads/stderr.txt.offset
- path: miniwdl_run/call-clean_check_reads/stdout.txt
- md5sum: 9e807ce699271c3f647c7594df2b5b0a
+ md5sum: 73809db947c875bf81acccaad76a57d5
- path: miniwdl_run/call-clean_check_reads/task.log
contains: ["wdl", "theiaprok_illumina_se", "check_reads", "done"]
- path: miniwdl_run/call-clean_check_reads/work/EST_GENOME_LENGTH
@@ -355,7 +355,7 @@
- path: miniwdl_run/call-quast/work/transposed_report.txt
contains: ["Assembly", "length", "contigs", "test"]
- path: miniwdl_run/call-raw_check_reads/command
- md5sum: 3f6bf93b769ef9b152f005195cf2502e
+ md5sum: 7594079920cccbcf01d027547f54ccc2
- path: miniwdl_run/call-raw_check_reads/inputs.json
contains: ["read1", "fastq", "skip_screen", "true"]
- path: miniwdl_run/call-raw_check_reads/outputs.json
@@ -364,7 +364,7 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: miniwdl_run/call-raw_check_reads/stderr.txt.offset
- path: miniwdl_run/call-raw_check_reads/stdout.txt
- md5sum: 9e807ce699271c3f647c7594df2b5b0a
+ md5sum: 73809db947c875bf81acccaad76a57d5
- path: miniwdl_run/call-raw_check_reads/task.log
contains: ["wdl", "theiaprok_illumina_se", "check_reads", "done"]
- path: miniwdl_run/call-raw_check_reads/work/EST_GENOME_LENGTH
@@ -526,7 +526,7 @@
- path: miniwdl_run/wdl/tasks/gene_typing/drug_resistance/task_resfinder.wdl
md5sum: 27528633723303b462d095b642649453
- path: miniwdl_run/wdl/tasks/gene_typing/variant_detection/task_snippy_variants.wdl
- md5sum: 284ce680b52e7e1c1753537b344fa161
+ md5sum: 3b9e04569d7e856dcc649b7726b306b7
- path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_bbduk.wdl
md5sum: aec6ef024d6dff31723f44290f6b9cf5
- path: miniwdl_run/wdl/tasks/quality_control/advanced_metrics/task_busco.wdl
@@ -544,7 +544,7 @@
- path: miniwdl_run/wdl/tasks/quality_control/basic_statistics/task_quast.wdl
contains: ["version", "quast", "output"]
- path: miniwdl_run/wdl/tasks/quality_control/comparisons/task_screen.wdl
- md5sum: 75631c4db89792a939e4d872adc05b86
+ md5sum: adb43c5bf0a83b9e2ef7669ed2d1760f
- path: miniwdl_run/wdl/tasks/quality_control/read_filtering/task_trimmomatic.wdl
contains: ["version", "trimmomatic", "output"]
- path: miniwdl_run/wdl/tasks/species_typing/escherichia_shigella/task_ectyper.wdl
@@ -596,7 +596,7 @@
- path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
md5sum: 5aa25e4fad466f92c96a7c138aca0d20
- path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl
- md5sum: 8ab95440118d06dd3c07765a19e876e7
+ md5sum: 670f990128063eb3c7b3fa49302f08b7
- path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl
md5sum: d11bfe33fdd96eab28892be5a01c1c7d
- path: miniwdl_run/workflow.log
diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl
index 690086a60..1d6914e79 100644
--- a/workflows/utilities/wf_merlin_magic.wdl
+++ b/workflows/utilities/wf_merlin_magic.wdl
@@ -631,7 +631,7 @@ workflow merlin_magic {
samplename = samplename,
snippy_variants_results = snippy_cauris.snippy_variants_results,
reference = cladetyper.clade_spec_ref,
- query_gene = select_first([snippy_query_gene, "FKS1,lanosterol.14-alpha.demethylase,uracil.phosphoribosyltransferase"]),
+ query_gene = select_first([snippy_query_gene, "FKS1,lanosterol.14-alpha.demethylase,uracil.phosphoribosyltransferase,B9J08_005340,B9J08_000401,B9J08_003102,B9J08_003737,B9J08_005343"]),
docker = snippy_gene_query_docker_image
}
}
@@ -976,7 +976,7 @@ workflow merlin_magic {
String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_crypto.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"])
- String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"])
+ String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_variants, "No matching taxon detected"])
String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, "No matching taxon detected"])
}
}
\ No newline at end of file