[New Workflow] AMR-search for neisseria gonorrhoeae samples #743
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| Original file line number | Diff line number | Diff line change |
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| # AMR Search | ||
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| ## Quick Facts | ||
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| | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | | ||
| |---|---|---|---|---| | ||
| | [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | vX.X.X | Yes | Sample-level | | ||
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| ## AMR_Search_PHB | ||
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| The AMR_Search workflow is a standalone version of Pathogenwatch's AMR profiling functionality utilizing `AMRsearch` tool from Pathogenwatch. | ||
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| A limited number of species are currently supported and are listed below. NCBI codes are needed from this table to select the correct library. | ||
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| | Species | NCBI Code | | ||
| |------------------------------|-----------| | ||
| | _Neisseria gonorrhoeae_ | 485 | | ||
| | _Staphylococcus aureus_ | 1280 | | ||
| | _Salmonella_ Typhi | 90370 | | ||
| | _Streptococcus pneumoniae_ | 1313 | | ||
| | _Klebisiella_ | 570 | | ||
| | _Escherichia_ | 561 | | ||
| | _Mycobacterium tuberculosis_ | 1773 | | ||
| | _Candida auris_ | 498019 | | ||
| | _Vibrio cholerae_ | 666 | | ||
| | _Campylobacter_ | 194 | | ||
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| !!! caption "AMR_Search Workflow Diagram" | ||
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| ### Inputs | ||
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| Input should be ordered as they appear on Terra | ||
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| | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** | | ||
| |---|---|---|---|---|---| | ||
| | amr_search_workflow | **amr_search_database** | String | NCBI taxon code of samples known taxonomy, see above supported species || Required | | ||
| | amr_search_workflow | **input_fasta** | File | A microbial assembly file || Required | | ||
| | amr_search_workflow | **samplename** | String | Identifier user wants prefixed to output files || Required | | ||
| | amr_search | **cpu** | Integer | Number of CPUs to allocate to the task |2| Optional | | ||
| | amr_search | **disk_size** | Integer | Amount of storage (in GB) to allocate to the task |50| Optional | | ||
| | amr_search | **docker** | String | The docker container to use for the task |us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.0| Optional | | ||
| | amr_search | **memory** | Integer | Amount of memory/RAM (in GB) to allocate to the task |8| Optional | | ||
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| ### Workflow Tasks | ||
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| Description of the workflow tasks | ||
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| ??? task "`amr_search`: Antimicrobial resistance profiling" | ||
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| This task performs *in silico* antimicrobial resistance (AMR) profiling for supported species using **AMRsearch**, the primary tool used by [Pathogenwatch](https://pathogen.watch/) to genotype and infer antimicrobial resistance (AMR) phenotypes from assembled microbial genomes. | ||
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| **AMRsearch** screens against Pathogenwatch's library of curated genotypes and inferred phenotypes, developed in collaboration with community experts. Resistance phenotypes are determined based on both **resistance genes** and **mutations**, and the system accounts for interactions between multiple SNPs, genes, and suppressors. Predictions follow **S/I/R classification** (*Sensitive, Intermediate, Resistant*). | ||
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| **Outputs:** | ||
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| - **JSON Output:** Contains the complete AMR profile, including detailed **resistance state**, detected **resistance genes/mutations**, and supporting **BLAST results**. | ||
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| - **CSV & PNG Tables:** An incorprated Python script, `parse_amr_json.py`, extracts and formats results into a **CSV file** and **PNG summary table** for easier visualization. | ||
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| !!! techdetails "amr_search Technical Details" | ||
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| | | Links | | ||
| | --- | --- | | ||
| | Task | [task_amr_search.wdl](https://github.com/theiagen/public_health_bioinformatics/blob/fc-amr-search-dev/tasks/gene_typing/drug_resistance/task_amr_search.wdl) | | ||
| | Software Source Code | [AMRsearch](https://github.com/pathogenwatch-oss/amr-search) | | ||
| | Software Documentation | [Pathogenwatch](https://cgps.gitbook.io/pathogenwatch) | | ||
| | Original Publication(s) | [PAARSNP: *rapid genotypic resistance prediction for *Neisseria gonorrhoeae*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545138/) | | ||
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| ### Outputs | ||
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| | **Variable** | **Type** | **Description** | | ||
| |---|---|---| | ||
| | amr_results_csv | File | CSV formatted AMR profile | | ||
| | amr_results_png | File | PNG formatted AMR profile | | ||
| | amr_search_results | File | JSON formatted AMR profile including BLAST results | | ||
| | amr_search_docker | String | Docker image used to run AMR_Search | | ||
| | amr_search_version | String | Version of AMR_Search libraries used | | ||
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| ## References | ||
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| > [Pathogenwatch AMRsearch](https://github.com/pathogenwatch-oss/amr-search) | ||
| <!-- --> | ||
| > [PAARSNP](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545138/) |
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| Original file line number | Diff line number | Diff line change |
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| version 1.0 | ||
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| task amr_search { | ||
| input { | ||
| File input_fasta | ||
| String samplename | ||
| String amr_search_database = "485" | ||
| String docker = "us-docker.pkg.dev/general-theiagen/theiagen/amrsearch:0.2.0" | ||
| Int cpu = 2 | ||
| Int disk_size = 50 | ||
| Int memory = 8 | ||
| } | ||
| command <<< | ||
| # Extract base name without path or extension | ||
| input_base=$(basename ~{input_fasta}) | ||
| input_base=${input_base%.*} | ||
| echo "DEBUG: input_base = $input_base" | ||
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| # Run the tool | ||
| java -jar /paarsnp/paarsnp.jar \ | ||
| -i ~{input_fasta} \ | ||
| -s ~{amr_search_database} | ||
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| # Move the output file from the input directory to the working directory | ||
| mv $(dirname ~{input_fasta})/${input_base}_paarsnp.jsn ./~{samplename}_paarsnp_results.jsn | ||
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| # Script housed within the image; https://github.com/theiagen/theiagen_docker_builds/tree/awh-amrsearch-image/amrsearch/0.0.20 | ||
| python3 /scripts/parse_amr_json.py \ | ||
| ./~{samplename}_paarsnp_results.jsn \ | ||
| ~{samplename} | ||
| >>> | ||
| output { | ||
| File json_output = "~{samplename}_paarsnp_results.jsn" | ||
| File output_csv = "~{samplename}_amr_results.csv" | ||
| File output_png = "~{samplename}_amr_results.png" | ||
| File output_version = "output_amr_version.txt" | ||
| String amr_search_docker = docker | ||
| } | ||
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| runtime { | ||
| memory: "~{memory} GB" | ||
| cpu: cpu | ||
| docker: docker | ||
| disks: "local-disk " + disk_size + " SSD" | ||
| maxRetries: 1 | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,27 @@ | ||
| version 1.0 | ||
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| import "../../tasks/gene_typing/drug_resistance/task_amr_search.wdl" as run_amr_search | ||
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| workflow amr_search_workflow { | ||
| input { | ||
| File input_fasta | ||
| String amr_search_database | ||
|
There was a problem hiding this comment. Please consider changing this as the user doesn't need to pass in a DB, only the taxon code that then references the correct DB to use. Taxon/taxon_of_interest/taxon_code might make more sense. Some of this will depend on how we do the mapping when we plug into TheiaProk, but just dropping this as a note for future work when we implement that integration upstream. |
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| String samplename | ||
| } | ||
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| # Call amr_search task to perform the analysis | ||
| call run_amr_search.amr_search { | ||
| input: | ||
| input_fasta = input_fasta, | ||
| samplename = samplename, | ||
| amr_search_database = amr_search_database | ||
| } | ||
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| output { | ||
| File amr_search_results = amr_search.json_output | ||
| File amr_results_csv = amr_search.output_csv | ||
| File amr_results_png = amr_search.output_png | ||
| String amr_search_docker = amr_search.amr_search_docker | ||
| String amr_search_version = read_string(amr_search.output_version) | ||
| } | ||
| } | ||
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maybe worth a comment here with a link to the location of this script, for posterity's sake
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Sounds good! Ill put the link to the current dev branch of the docker builds repo and will update it when it gets merged.