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Update v0.2 workflow (#14)
* Add updated workflow * Update workflow diagram * Use updated bracken adjustment tool * Add krona chart * Fix unit tests * whitespace * Capture top 5 species, set default confidence to 0.1 * Add proportion_unclassified to table of metadata fields * whitespace
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‎README.md

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@@ -32,12 +32,15 @@ This can be used to estimate the relative abundance of sequence reads originatin
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In order to use this pipeline, you will also have to install the [kraken2][] and [bracken][] Galaxy tools and their data
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managers within your Galaxy instance. These can be found at:
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| Name | Version | Revision |
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|------------------------------------|-----------------------|--------------------------------------------------------------------------------------------|
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| kraken2 | `2.1.1+galaxy1` | [`e674066930b2`](https://toolshed.g2.bx.psu.edu/view/iuc/kraken2/e674066930b2) |
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| bracken | `2.6.1+galaxy0` | [`b08ac10aed96`](https://toolshed.g2.bx.psu.edu/view/iuc/bracken/b08ac10aed96) |
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| data_manager_build_kraken2_database| `2.1.1` | [`2f27f3b86827`](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/2f27f3b86827) |
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| data_manager_build_bracken_database| `2.5.1+galaxy1` | [`3c7d2c84cb09`](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_bracken_database/3c7d2c84cb09) |
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| Name | Version | Owner | Metadata Revision | Galaxy Toolshed Link |
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|---------------------------------------|------------------|--------------------------------|-------------------|----------------------------------------|
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| fastp | `0.23.2+galaxy0` | `iuc` | 10 (2022-02-03) | [fastp-10:65b93b623c77](https://toolshed.g2.bx.psu.edu/view/iuc/fastp/65b93b623c77) |
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| fastp_json_to_tabular | `0.1.0` | `public-health-bioinformatics` | 0 (2022-03-10) | [fastp_json_to_tabular-0:091a2fb2e7ad](https://toolshed.g2.bx.psu.edu/view/public-health-bioinformatics/fastp_json_to_tabular/091a2fb2e7ad) |
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| kraken2 | `2.1.1+galaxy1` | `iuc` | 4 (2021-02-17) | [kraken2-4:e674066930b2](https://toolshed.g2.bx.psu.edu/view/iuc/kraken2/e674066930b2) |
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| bracken | `2.6.1+galaxy0` | `iuc` | 4 (2021-06-07) | [bracken-4:b08ac10aed96](https://toolshed.g2.bx.psu.edu/view/iuc/bracken/b08ac10aed96) |
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| adjust_bracken_for_unclassified_reads | `0.1.0` | `public-health-bioinformatics` | 1 (2021-03-10) | [adjust_bracken_for_unclassified_reads-1:3cde438eb222](https://toolshed.g2.bx.psu.edu/view/iuc/bracken/b08ac10aed96) |
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| data_manager_build_kraken2_database | `2.1.2+galaxy0` | `iuc` | 6 (2022-06-24) | [`data_manager_build_kraken2_database-6:9002633b4737`](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_kraken2_database/9002633b4737) |
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| data_manager_build_bracken_database | `2.5.1+galaxy1` | `iuc` | 3 (2021-11-08) | [`data_manager_build_bracken_database-3:3c7d2c84cb09`](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_build_bracken_database/3c7d2c84cb09) |
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## Preparing Databases
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And, you should be able to save and view these results in the IRIDA metadata table. The following fields are written to
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the IRIDA 'Line List':
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| Field Name | Description |
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|--------------------------------------|-------------------------------------------------------------------------------------|
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| `species-abundance/taxonomy_level` | The taxonomic level at which reads were aggregated ('S' for species) |
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| `species-abundance/taxon_name` | The scientific name of the most abundant species in the sample |
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| `species-abundance/taxonomy_id` | The NCBI taxonomy ID for the most abundant species in the sample |
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| `species-abundance/proportion` | The proportion of reads in this sample assigned to the most abundant species |
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| `species-abundance/taxon_name_2` | The scientific name of the second-most abundant species in the sample |
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| `species-abundance/taxonomy_id_2` | The NCBI taxonomy ID for the second-most abundant species in the sample |
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| `species-abundance/proportion_2` | The proportion of reads in this sample assigned to the second-most abundant species |
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| `species-abundance/taxon_name_3` | The scientific name of the third-most abundant species in the sample |
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| `species-abundance/taxonomy_id_3` | The NCBI taxonomy ID for the third-most abundant species in the sample |
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| `species-abundance/proportion_3` | The proportion of reads in this sample assigned to the third-most abundant species |
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| `species-abundance/taxon_name_4` | The scientific name of the fourth-most abundant species in the sample |
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| `species-abundance/taxonomy_id_4` | The NCBI taxonomy ID for the fourth-most abundant species in the sample |
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| `species-abundance/proportion_4` | The proportion of reads in this sample assigned to the fourth-most abundant species |
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| `species-abundance/taxon_name_5` | The scientific name of the fifth-most abundant species in the sample |
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| `species-abundance/taxonomy_id_5` | The NCBI taxonomy ID for the fifth-most abundant species in the sample |
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| `species-abundance/proportion_5` | The proportion of reads in this sample assigned to the fifth-most abundant species |
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| Field Name | Description |
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|---------------------------------------------|-------------------------------------------------------------------------------------|
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| `species-abundance/taxonomy_level` | The taxonomic level at which reads were aggregated ('S' for species) |
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| `species-abundance/taxon_name` | The scientific name of the most abundant species in the sample |
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| `species-abundance/taxonomy_id` | The NCBI taxonomy ID for the most abundant species in the sample |
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| `species-abundance/proportion` | The proportion of reads in this sample assigned to the most abundant species |
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| `species-abundance/taxon_name_2` | The scientific name of the second-most abundant species in the sample |
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| `species-abundance/taxonomy_id_2` | The NCBI taxonomy ID for the second-most abundant species in the sample |
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| `species-abundance/proportion_2` | The proportion of reads in this sample assigned to the second-most abundant species |
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| `species-abundance/taxon_name_3` | The scientific name of the third-most abundant species in the sample |
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| `species-abundance/taxonomy_id_3` | The NCBI taxonomy ID for the third-most abundant species in the sample |
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| `species-abundance/proportion_3` | The proportion of reads in this sample assigned to the third-most abundant species |
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| `species-abundance/taxon_name_4` | The scientific name of the fourth-most abundant species in the sample |
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| `species-abundance/taxonomy_id_4` | The NCBI taxonomy ID for the fourth-most abundant species in the sample |
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| `species-abundance/proportion_4` | The proportion of reads in this sample assigned to the fourth-most abundant species |
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| `species-abundance/taxon_name_5` | The scientific name of the fifth-most abundant species in the sample |
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| `species-abundance/taxonomy_id_5` | The NCBI taxonomy ID for the fifth-most abundant species in the sample |
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| `species-abundance/proportion_5` | The proportion of reads in this sample assigned to the fifth-most abundant species |
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| `species-abundance/proportion_unclassified` | The proportion of unclassified reads in the sample | |
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Note that by default, these fields will not appear in sorted order in the line list. Refer to the [IRIDA Documentation on metadata management](https://phac-nml.github.io/irida-documentation/user/user/sample-metadata/#project-metadata-line-list) to create a customized view of these fields.
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‎doc/images/galaxy-workflow-diagram.png

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‎src/main/java/org/publichealthbioinformatics/irida/plugin/speciesabundance/SpeciesAbundancePluginUpdater.java

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@@ -89,12 +89,16 @@ public void update(Collection<Sample> samples, AnalysisSubmission analysis) thro
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String workflowName = iridaWorkflow.getWorkflowDescription().getName();
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List<Map<String, String>> speciesAbundances = parseSpeciesAbundanceFile(speciesAbundanceFilePath);
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Map<String, String> unclassifiedAbundances = speciesAbundances.remove(0);
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String key;
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String value;
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PipelineProvidedMetadataEntry entry;
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value = unclassifiedAbundances.get("bracken_fraction_total_seqs");
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entry = new PipelineProvidedMetadataEntry(value, "float", analysis);
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key = workflowName + "/" + "proportion_unclassified";
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metadataEntries.put(key, entry);
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int speciesNum = 1;
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for (Map<String, String> species : speciesAbundances) {
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String key;
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String value;
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PipelineProvidedMetadataEntry entry;
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value = species.get("taxonomy_lvl");
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entry = new PipelineProvidedMetadataEntry(value, "text", analysis);
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// taxonomy_level is only recorded once per sample. (should be identical for all lines in a report.)
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}
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metadataEntries.put(key, entry);
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value = species.get("fraction_total_reads");
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value = species.get("bracken_fraction_total_seqs");
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entry = new PipelineProvidedMetadataEntry(value, "float", analysis);
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if (speciesNum == 1) {
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key = workflowName + "/" + "proportion";
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* should look like:
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*
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* <pre>
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* name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads
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* Salmonella enterica 28901 S 433515 32457 465972 0.99016
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* name taxonomy_id taxonomy_lvl kraken_assigned_seqs bracken_assigned_seqs total_seqs kraken_fraction_total_seqs bracken_fraction_total_seqs
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* Salmonella enterica 28901 S 228436 841169 848138 0.269338 0.991783
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* </pre>
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*
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* @return A {@link Map<String, String>} containing the read count.
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BufferedReader speciesAbundanceReader = new BufferedReader(new FileReader(speciesAbundanceFilePath.toFile()));
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List<Map<String, String>> abundances = new ArrayList<>();
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ArrayList<String> expectedHeaderFields = new ArrayList<String>(Arrays.asList(
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"name",
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"name",
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"taxonomy_id",
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"taxonomy_lvl",
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"kraken_assigned_reads",
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"added_reads",
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"new_est_reads",
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"fraction_total_reads"
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"kraken_assigned_seqs",
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"bracken_assigned_seqs",
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"total_seqs",
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"kraken_fraction_total_seqs",
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"bracken_fraction_total_seqs"
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));
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try {
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String headerLine = speciesAbundanceReader.readLine();
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}
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abundances.add(speciesAbundanceMap);
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}
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for (int i = 0; i < (NUM_SPECIES_TO_REPORT - 1); i++) {
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for (int i = 0; i < NUM_SPECIES_TO_REPORT; i++) {
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abundancesLine = speciesAbundanceReader.readLine();
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ArrayList<String> speciesAbundanceFields = new ArrayList<String>(Arrays.asList(abundancesLine.split("\t")));
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Map<String, String> speciesAbundanceMap = new HashMap<>();

‎src/main/resources/workflows/0.2.0/irida_workflow.xml

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<requiresSingleSample>true</requiresSingleSample>
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</inputs>
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<parameters>
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<parameter name="kraken2-1-confidence" defaultValue="0.0">
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<parameter name="kraken2-1-confidence" defaultValue="0.1">
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<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1" parameterName="confidence" label="Confidence" type="float"/>
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</parameter>
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<parameter name="kraken2-1-kraken2_database" required="true">
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<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1" parameterName="min_base_quality" label="Minimum Base Quality" type="integer"/>
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</parameter>
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<parameter name="bracken-2-threshold" defaultValue="10">
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<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.6.1+galaxy0" parameterName="threshold"/>
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<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.7+galaxy0" parameterName="threshold"/>
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</parameter>
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<parameter name="bracken-2-kmer_distr" required="true">
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<dynamicSource>
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<galaxyToolDataTable name="bracken_databases" displayColumn="name" parameterColumn="value" />
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</dynamicSource>
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<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.6.1+galaxy0" parameterName="kmer_distr"/>
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<toolParameter toolId="toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.7+galaxy0" parameterName="kmer_distr"/>
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</parameter>
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</parameters>
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<outputs>
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<output name="fastp_report" fileName="fastp_report.html" />
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<output name="fastp_json" fileName="fastp.json" />
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<output name="species_abundance" fileName="species_abundance.tsv" />
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<output name="kraken2_report" fileName="kraken2_report.tsv" />
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<output name="krona_chart" fileName="krona_chart.html" />
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</outputs>
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<toolRepositories>
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<repository>
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<name>fastp</name>
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<owner>iuc</owner>
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<url>https://toolshed.g2.bx.psu.edu</url>
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<revision>65b93b623c77</revision>
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</repository>
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<repository>
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<name>fastp_json_to_tabular</name>
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<owner>public-health-bioinformatics</owner>
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<url>https://toolshed.g2.bx.psu.edu</url>
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<revision>091a2fb2e7ad</revision>
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</repository>
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<repository>
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<name>kraken2</name>
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<owner>iuc</owner>
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<url>https://toolshed.g2.bx.psu.edu</url>
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<revision>b08ac10aed96</revision>
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</repository>
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<repository>
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<name>adjust_bracken_for_unclassified_reads</name>
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<owner>public-health-bioinformatics</owner>
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<url>https://toolshed.g2.bx.psu.edu</url>
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<revision>899a650587ed</revision>
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</repository>
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<repository>
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<name>krakentools</name>
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<owner>jvolkening</owner>
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<url>https://toolshed.g2.bx.psu.edu</url>
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<revision>d491c23394f9</revision>
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</repository>
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<repository>
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<name>taxonomy_krona_chart</name>
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<owner>crs4</owner>
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<url>https://toolshed.g2.bx.psu.edu</url>
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<revision>e9005d1f3cfd</revision>
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</repository>
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<repository>
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<name>data_manager_build_kraken2_database</name>
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<owner>iuc</owner>
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<url>https://toolshed.g2.bx.psu.edu</url>
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<revision>2f27f3b86827</revision>
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<revision>9002633b4737</revision>
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</repository>
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<repository>
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<name>data_manager_build_bracken_database</name>

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