diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml new file mode 100644 index 000000000..2031035d2 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.dockstore.yml @@ -0,0 +1,25 @@ +version: 1.2 +workflows: +- name: QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga + testParameterFiles: + - /QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" + +- name: QIIME2-VI-diversity-metrics-and-estimations + subclass: Galaxy + publish: true + primaryDescriptorPath: /QIIME2-VI-diversity-metrics-and-estimations.ga + testParameterFiles: + - /QIIME2-VI-diversity-metrics-and-estimations-tests.yml + authors: + - name: Debjyoti Ghosh + orcid: 0009-0008-1496-1677 + - name: "Helmholtz-Zentrum für Umweltforschung - UFZ" + address: "Permoserstraße 15, 04318 Leipzig" \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml new file mode 100644 index 000000000..2a1023efd --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/.workflowhub.yml @@ -0,0 +1,5 @@ +version: '0.1' +registries: +- url: https://workflowhub.eu + project: iwc + workflow: qiime2/main diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md new file mode 100644 index 000000000..7df9c9552 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/CHANGELOG.md @@ -0,0 +1,4 @@ +# Changelog + +## [0.1] 2024-06-22 +First release. \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml new file mode 100644 index 000000000..b5cf8d512 --- /dev/null +++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis-tests.yml @@ -0,0 +1,108 @@ +- doc: Test outline for QIIME2-III:-Phylogenetic-tree-for-diversity-analysis + job: + Metadata: + class: File + location: https://data.qiime2.org/2024.2/tutorials/pd-mice/sample_metadata.tsv + filetype: tabular + Representative sequences: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_rep_set.qza + filetype: qza + Feature table: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/dada2_table.qza + filetype: qza + Minimum depth: 1 + Maximum depth: 2019 + Taxonomic classifier: + class: File + location: https://docs.qiime2.org/2024.2/data/tutorials/pd-mice/gg-13-8-99-515-806-nb-classifier.qza + filetype: qza + SEPP fragment insertion reference: + class: File + location: https://data.qiime2.org/2024.2/common/sepp-refs-gg-13-8.qza + filetype: qza + outputs: + Rooted tree: + ftype: qza + asserts: + - has_size: + min: 2M + max: 3M + - has_archive_member: + path: "^[^/]*/data/tree.nwk" + n: 1 + asserts: + - has_text_matching: + expression: "k__Bacteria" + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: Phylogeny[Rooted]" + - has_line: + line: "format: NewickDirectoryFormat" + + Rarefaction curve: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/index.html" + n: 1 + # data per measure + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 3 + # data for each measure and metadata variable (*7) + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 21 + + Taxonomy classification: + ftype: qza + asserts: + - has_size: + min: 70k + max: 80k + - has_archive_member: + path: "^[^/]*/metadata.yaml" + n: 1 + asserts: + - has_line: + line: "type: FeatureData[Taxonomy]" + - has_line: + line: "format: TSVTaxonomyDirectoryFormat" + - has_archive_member: + path: "^[^/]*/data/taxonomy.tsv" + n: 1 + asserts: + - has_n_lines: + n: 288 + Taxa barplot: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/.*\\.csv" + n: 7 + - has_archive_member: + path: "^[^/]*/data/.*\\.jsonp" + n: 7 + Taxonomy classification table: + ftype: qza + asserts: + - has_size: + min: 1M + max: 2M + - has_archive_member: + path: "^[^/]*/data/metadata.tsv" + n: 1 + asserts: + - has_n_lines: + n: 289 \ No newline at end of file diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis.ga 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+ path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Alpha diversity - Observed features: + ftype: qzv + asserts: + - has_size: + min: 300k + max: 400k + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.csv" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.jsonp" + n: 6 + Beta diversity - Bray-Curtis distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Beta diversity - Jaccard distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Beta diversity - weighted UniFrac distance metrics: + ftype: qzv + asserts: + - has_size: + min: 400k + max: 500k + - has_archive_member: + path: "^[^/]*/data/raw_data\\.tsv" + n: 1 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.png" + n: 6 + - has_archive_member: + path: "^[^/]*/data/[^/]*\\.pdf" + n: 6 + Emperor plot collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + Distance matrix collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + PCoA collection: + element_tests: + 'unweighted_unifrac': + ftype: qzv + 'weighted_unifrac': + ftype: qzv + 'jaccard': + ftype: qzv + 'bray_curtis': + ftype: qzv + Richness and evenness collection: + element_tests: + 'rarefied_table': + ftype: qzv + 'faith_pd_vector': + ftype: qzv + 'observed_features_vector': + ftype: qzv + 'shannon_vector': + ftype: qzv + 'eveness_vector': + ftype: qzv \ No newline at end of file diff --git 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diversity analysis, IV) rarefaction analysis, V) taxonomic analysis. +- VI: Computation of diversity metrics and estimations + +Analogous to the procedures described in the Parkinson’s Mouse Tutorial: https://docs.qiime2.org/2024.5/tutorials/pd-mice/ + +## Inputs + +The two workflows have two inputs in common + +- Feature table: Count data +- Metadata: Metadata table + +and the following extra inputs + +III-V + +- Representative sequences: Representative (ASV) sequences +- Minimum depth: Lower limit of the sampling depth for the alpha rarefaction analysis +- Maximum depth: Upper limit of the sampling depth for the alpha rarefaction analysis +- SEPP fragment insertion reference: used for the reconstruction of the phylogenetic tree +- Taxonomic classifier: The classifier to assign taxonomic information to the ASVs + +VI: + +Sampling depth: For the metric calculation (should be based on the rarefaction analysis done in IV) +Target metadata parameter: that should be used for beta diversity calculations +Rooted Tree: for instance the tree computed in III + +## Processing + +III-V + +- Phylogenetic tree generation using `qiime2 fragment-insertion sepp` +- Alpha rarefaction analysis using `qiime2 diversity alpha-rarefaction` +- Taxonomic classification using `qiime2 feature-classifier classify-sklearn` and compute barplot and tabular output + +VI: + +- compute alpha and beta diversity metrics using `qiime2 diversity core-metrics-phylogenetic` +- organize these metrics in 4 collections: + 1. Distance matrix collection (weighted and unweighted unifrac, jaccard and bray curtis) + 2. PCoA collection (same as the distance matrices) + 3. Emperor plot collection (same as the distance matrices) + 4. Richness and evenness collection (rarefied table, faith pd vector observed features vector, shannon vector, evenness vector) +- get visualization for alpha diversity: + - Pielou's eveness + - Observed features + - Shannons diversity index +- get visualization for beta diversity + - Jaccard distance matrix + - Bray curtis distance matrix + - Unifrac distance metrix + +## Outputs + +III-V: + +- Phylogenetic tree +- Rarefaction curve +- Taxonomic classification (as qza, barplot and table) + +VI: + +- Four collections containing: distance matrix, PCoA, Emperor plots, Richness and evenness +- Visualization for alpha diversity: Pielou's eveness, Observed features, Shannons diversity index +- Visualization for beta diversity: Jaccard, Bray curtis, Unifrac \ No newline at end of file