Add Influenza isolate subtyping

workflows/virology/influenza-isolate-subtyping/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /influenza-isolate-subtyping.ga
+  testParameterFiles:
+  - /influenza-isolate-subtyping-test.yml
+  authors:
+  - name: Viktoria Isabel Schwarz
+    orcid: 0000-0001-6897-1215
+  - name: Wolfgang Maier
+    orcid: 0000-0002-9464-6640

workflows/virology/influenza-isolate-subtyping/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2025-01-09
+
+First release.

workflows/virology/influenza-isolate-subtyping/README.md

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+# Influenza Isolate Subtyping workflow
+
+This workflow facilitates Influenza A isolate subtyping and consensus sequence generation using the VAPOR tool. It takes as input a collection of reference sequences for each viral segment and FASTQ files containing sequencing reads.
+

workflows/virology/influenza-isolate-subtyping/influenza-isolate-subtyping-test.yml

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+- doc: Test outline for influenza-isolate-subtyping.ga
+  job:
+    References per segment collection:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: ref_1_pb2
+        location: https://zenodo.org/records/14628364/files/ref_1_pb2.fasta
+        filetype: fasta
+      - class: File
+        identifier: ref_2_pb1
+        location: https://zenodo.org/records/14628364/files/ref_2_pb1.fasta
+        filetype: fasta
+      - class: File
+        identifier: ref_3_pa
+        location: https://zenodo.org/records/14628364/files/ref_3_pa.fasta
+        filetype: fasta
+      - class: File
+        identifier: ref_4_ha
+        location: https://zenodo.org/records/14628364/files/ref_4_ha.fasta
+        filetype: fasta
+      - class: File
+        identifier: ref_5_np
+        location: https://zenodo.org/records/14628364/files/ref_5_np.fasta
+        filetype: fasta
+      - class: File
+        identifier: ref_6_na
+        location: https://zenodo.org/records/14628364/files/ref_6_na.fasta
+        filetype: fasta
+      - class: File
+        identifier: ref_7_mp
+        location: https://zenodo.org/records/14628364/files/ref_7_mp.fasta
+        filetype: fasta
+      - class: File
+        identifier: ref_8_ns
+        location: https://zenodo.org/records/14628364/files/ref_8_ns.fasta
+        filetype: fasta
+    Sequenced paired-end data:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: SRR24839074
+        elements:
+        - identifier: forward
+          class: File
+          location: https://zenodo.org/records/14628364/files/SRR24839074_1.fastq.gz
+          filetype: fastqsanger.gz
+        - identifier: reverse
+          class: File
+          location: https://zenodo.org/records/14628364/files/SRR24839074_2.fastq.gz
+          filetype: fastqsanger.gz
+      - class: Collection
+        type: paired
+        identifier: SRR6674560
+        elements:
+        - identifier: forward
+          class: File
+          location: https://zenodo.org/records/14628364/files/SRR6674560_1.fastq.gz
+          filetype: fastqsanger.gz
+        - identifier: reverse
+          class: File
+          location: https://zenodo.org/records/14628364/files/SRR6674560_2.fastq.gz
+          filetype: fastqsanger.gz
+  outputs:
+    subtyping_results:
+      asserts:
+        has_n_lines:
+          n: 2
+        has_n_columns:
+          n: 2
+        has_text:
+          text: "SRR6674560\tH3N2"
+          text: "SRR24839074\tH5N1"
+    fastp_html:
+      element_tests:
+        SRR6674560:
+          asserts:
+            has_text:
+              text: "<tbody><tr><td class=\"col1\">total reads:</td><td class=\"col2\">345.266000 K</td></tr>"
+    vapor_closest_references:
+      element_tests:
+        SRR6674560:
+          elements:
+            ref_1_pb2:
+              asserts:
+                has_text:
+                  text: "0.9912280701754386\t6353408.0\t2280\t2786.582456140351\t31588\t>PB2|A/Texas/50/2012|A/H3N2|KJ942623.1"
+            ref_2_pb1:
+              asserts:
+                has_text:
+                  text: "0.9938515590689504\t5162362.0\t2277\t2267.176987263944\t25586\t>PB1|A/Texas/50/2012|A/H3N2|KJ942622.1"
+            ref_3_pa:
+              asserts:
+                has_text:
+                  text: "0.99302649930265\t4983278.0\t2151\t2316.7261738726174\t24765\t>PA|A/Netherlands/10407/2018|A/H1N2"
+            ref_4_ha:
+              asserts:
+                has_text:
+                  text: "0.9841269841269841\t12026563.0\t1701\t7070.289829512052\t60505\t>HA|A/Texas/50/2012|A/H3N2|KJ942616.1"
+            ref_5_np:
+              asserts:
+                has_text:
+                  text: "0.9933199732798931\t9583550.0\t1497\t6401.837007348029\t47910\t>NP|A/Texas/50/2012|A/H3N2|KJ942619.1"
+            ref_6_na:
+              asserts:
+                has_text:
+                  text: "0.9929078014184397\t6935928.0\t1410\t4919.097872340426\t34376\t>NA|A/Texas/50/2012|A/H3N2|KJ942618.1"
+            ref_7_mp:
+              asserts:
+                has_text:
+                  text: "1.0\t13252717.0\t982\t13495.63849287169\t66742\t>MP|A/Victoria/361/2011|A/H3N2|KJ942681.1"
+            ref_8_ns:
+              asserts:
+                has_text:
+                  text: "0.9952267303102625\t10526974.0\t838\t12562.021479713603\t52978\t>NS|A/Texas/50/2012|A/H3N2|KJ942620.1"
+    per_sample_consensus_sequences:
+      element_tests:
+        SRR6674560:
+          elements:
+            PB2:
+              asserts:
+                has_text:
+                  text: ">Consensus_PB2_threshold_0.7_quality_20"
+            PB1:
+              asserts:
+                has_text:
+                  text: ">Consensus_PB1_threshold_0.7_quality_20"
+            PA:
+              asserts:
+                has_text:
+                  text: ">Consensus_PA_threshold_0.7_quality_20"
+            HA:
+              asserts:
+                has_text:
+                  text: ">Consensus_HA_threshold_0.7_quality_20"
+            NP:
+              asserts:
+                has_text:
+                  text: ">Consensus_NP_threshold_0.7_quality_20"
+            NA:
+              asserts:
+                has_text:
+                  text: ">Consensus_NA_threshold_0.7_quality_20"
+            MP:
+              asserts:
+                has_text:
+                  text: ">Consensus_MP_threshold_0.7_quality_20"
+            NS:
+              asserts:
+                has_text:
+                  text: ">Consensus_NS_threshold_0.7_quality_20"
+    per_segment_samples_combined_consensus:
+      element_tests:
+        PB2:
+          asserts:
+            has_text:
+              text: ">SRR6674560|PB2"
+              text: ">SRR24839074|PB2"
+        PB1:
+          asserts:
+            has_text:
+              text: ">SRR6674560|PB1"
+              text: ">SRR24839074|PB1"
+        PA:
+          asserts:
+            has_text:
+              text: ">SRR6674560|PA"
+              text: ">SRR24839074|PA"
+        HA:
+          asserts:
+            has_text:
+              text: ">SRR6674560|HA"
+              text: ">SRR24839074|HA"
+        NP:
+          asserts:
+            has_text:
+              text: ">SRR6674560|NP"
+              text: ">SRR24839074|NP"
+        NA:
+          asserts:
+            has_text:
+              text: ">SRR6674560|NA"
+              text: ">SRR24839074|NA"
+        MP:
+          asserts:
+            has_text:
+              text: ">SRR6674560|MP"
+              text: ">SRR24839074|MP"
+        NS:
+          asserts:
+            has_text:
+              text: ">SRR6674560|NS"
+              text: ">SRR24839074|NS"
+    per_segment_snipit_plots:
+      element_tests:
+        PB2:
+          asserts:
+            has_size:
+              value: 571300
+              delta: 10000
+        PB1:
+          asserts:
+            has_size:
+              value: 548800
+              delta: 10000
+        PA:
+          asserts:
+            has_size:
+              value: 606800
+              delta: 10000
+        HA:
+          asserts:
+            has_size:
+              value: 961300
+              delta: 10000
+        NP:
+          asserts:
+            has_size:
+              value: 495700
+              delta: 10000
+        NA:
+          asserts:
+            has_size:
+              value: 809800
+              delta: 10000
+        MP:
+          asserts:
+            has_size:
+              value: 296100
+              delta: 10000
+        NS:
+          asserts:
+            has_size:
+              value: 278600
+              delta: 10000
+