QIIME2 workflows

workflows/amplicon/qiime2/README.md

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+# QIIME2 workflows
+
+## Available workflows
+
+1. Import of fastqsanger.gz data into QIIME artifact files. Available for
+   - paired / single end data
+   - demultiplexed / multiplexed data (the later according to the EMP protocol)
+   For data that is multiplexed with another protocol the cutadapt tool can be used.
+2. Denoising with DADA2
+   - paired / single end data

workflows/amplicon/qiime2/qiime2-I-import/.dockstore.yml

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+version: 1.2
+workflows:
+- name: QIIME2-Ia import multiplexed data single end
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /QIIME2-Ia-multiplexed-data-single-end.ga
+  testParameterFiles:
+  - /QIIME2-Ia-multiplexed-data-single-end-tests.yml
+  authors:
+  - name: Debjyoti Ghosh
+    orcid: 0009-0008-1496-1677
+  - name: "Helmholtz-Zentrum für Umweltforschung - UFZ"
+    address: "Permoserstraße 15, 04318 Leipzig"
+- name: QIIME2-Ib import multiplexed data paired end
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /QIIME2-Ib-multiplexed-data-paired-end.ga
+  testParameterFiles:
+  - /QIIME2-Ib-multiplexed-data-paired-end-tests.yml
+  authors:
+  - name: Debjyoti Ghosh
+    orcid: 0009-0008-1496-1677
+  - name: "Helmholtz-Zentrum für Umweltforschung - UFZ"
+    address: "Permoserstraße 15, 04318 Leipzig"
+- name: QIIME2-Ic import demultiplexed data single end
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /QIIME2-Ic-demultiplexed-data-single-end.ga
+  testParameterFiles:
+  - /QIIME2-Ic-demultiplexed-data-single-end-tests.yml
+  authors:
+  - name: Debjyoti Ghosh
+    orcid: 0009-0008-1496-1677
+  - name: "Helmholtz-Zentrum für Umweltforschung - UFZ"
+    address: "Permoserstraße 15, 04318 Leipzig"
+- name: QIIME2-Id import demultiplexed data paired end
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /QIIME2-Id-demultiplexed-data-paired-end.ga
+  testParameterFiles:
+  - /QIIME2-Id-demultiplexed-data-paired-end-tests.yml
+  authors:
+  - name: Debjyoti Ghosh
+    orcid: 0009-0008-1496-1677
+  - name: "Helmholtz-Zentrum für Umweltforschung - UFZ"
+    address: "Permoserstraße 15, 04318 Leipzig"
+

workflows/amplicon/qiime2/qiime2-I-import/.workflowhub.yml

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+version: '0.1'
+registries:
+- url: https://workflowhub.eu
+  project: iwc
+  workflow: qiime2/main

workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end-tests.yml

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+# test data from https://docs.qiime2.org/2024.2/tutorials/moving-pictures-usage/
+- doc: Test outline for QIIME2-Ia:-Demultiplexing-(single-end)
+  job:
+    Sequences:
+      class: File
+      location: https://data.qiime2.org/2024.2/tutorials/moving-pictures/emp-single-end-sequences/sequences.fastq.gz
+      filetype: fastqsanger.gz
+    Barcodes:
+      class: File
+      location: https://data.qiime2.org/2024.2/tutorials/moving-pictures/emp-single-end-sequences/barcodes.fastq.gz
+      filetype: fastqsanger.gz
+    Metadata:
+      class: File
+      location: https://data.qiime2.org/2024.2/tutorials/moving-pictures/sample_metadata.tsv
+      filetype: tabular
+    Metadata parameter: barcode-sequence
+    Reverse complement barcodes: false
+  outputs:
+    Demultiplexed single-end data:
+      asserts:
+        - has_size:
+            value: 20M
+            delta: 1M
+        - has_archive_member:
+            path: ".*data/L[0-9]S[0-9]{1,3}_[0-9]{1,2}_L001_R1_001\\.fastq\\.gz"
+            n: 34
+        - has_archive_member:
+            path: ".*/data/metadata.yml"
+            asserts:
+              - has_text:
+                  text: "phred-offset: 33"
+        - has_archive_member:
+            path: "^[^/]*/metadata.yaml"
+            n: 1
+            asserts:
+              - has_text:
+                  text: "uuid:"
+              - has_text:
+                  text: "type: SampleData[SequencesWithQuality]"
+              - has_text:
+                  text: "format: SingleLanePerSampleSingleEndFastqDirFmt"