Merge pull request #5339 from sujaikumar/sujaikumar-lotus2-identifyin…

…g-fungi

Add new ecology tutorial on identifying mycorrhizal fungi using lotus2 tool

CONTRIBUTORS.yaml

@@ -331,6 +331,10 @@ bernt-matthias:
     joined: 2017-09
     elixir_node: de
 
+bethanmanley:
+   name: Bethan Manley
+   joined: 2024-09
+
 bethlehem-adnew:
    name: Bethlehem Adnew
    joined: 2024-06
@@ -2229,6 +2233,10 @@ suchitrathapa:
     name: Suchitra Thapa
     joined: 2021-11
 
+sujaikumar:
+    name: Sujai Kumar
+    joined: 2024-09
+
 supernord:
     name: Johan Gustafsson
     joined: 2024-02

ORGANISATIONS.yaml

@@ -213,6 +213,12 @@ sciensano:
   github: false
   ror: "04ejags36"
 
+societyprotectionundergroundnetworks:
+    name: Society for the Protection of Underground Networks
+    description: "SPUN is a scientific research organization founded to map mycorrhizal fungal communities and advocate for their protection."
+    url: "https://www.spun.earth"
+    avatar: "/training-material/shared/images/spun-logo.png"
+
 swiss-tph:
     name: Swiss Tropical and Public Health Institute
     url: https://www.swisstph.ch/en/

topics/microbiome/tutorials/lotus2-identifying-fungi/tutorial.bib

@@ -0,0 +1,27 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{ozkurt2022,
+  title={LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis},
+  author={\"{O}zkurt,  Ezgi and Fritscher,  Joachim and Soranzo,  Nicola and Ng,  Duncan Y. K. and Davey,  Robert P. and Bahram,  Mohammad and Hildebrand,  Falk},
+  journal={Microbiome},
+  volume={10},
+  number={1},
+  year={2022},
+  publisher={Springer Science and Business Media LLC},
+  doi={10.1186/s40168-022-01365-1}
+}
+

topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/index.md

@@ -0,0 +1,3 @@
+---
+layout: workflow-list
+---

topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/lotus2-fungi-workflow-tests.yml

@@ -0,0 +1,53 @@
+- doc: Test outline for Workflow-for-Identifying-MF-from-ITS2-sequencing-using-LotuS2---tutorial-example-run'
+  job:
+    Mapping tsv:
+      class: File
+      path: https://zenodo.org/records/13710591/files/Colombia_ITS2_Mapping.tsv
+      filetype: tabular
+    sdm Options txt:
+      class: File
+      path: https://zenodo.org/records/13710591/files/sdm_miSeq_ITS.txt
+      filetype: txt
+    Input Dataset Collection:
+      class: Collection
+      collection_type: list:paired
+      elements:
+      - class: Collection
+        type: paired
+        identifier: C_ITS2_S160_001.fastq
+        elements:
+        - class: File
+          identifier: forward
+          path: https://zenodo.org/records/13710591/files/C_ITS2_S160_R1_001.fastq.gz
+        - class: File
+          identifier: reverse
+          path: https://zenodo.org/records/13710591/files/C_ITS2_S160_R2_001.fastq.gz
+      - class: Collection
+        type: paired
+        identifier: N5_ITS2_S140_001.fastq
+        elements:
+        - class: File
+          identifier: forward
+          path: https://zenodo.org/records/13710591/files/N5_ITS2_S140_R1_001.fastq.gz
+        - class: File
+          identifier: reverse
+          path: https://zenodo.org/records/13710591/files/N5_ITS2_S140_R2_001.fastq.gz
+      - class: Collection
+        type: paired
+        identifier: Pcov3_ITS2_S151_001.fastq
+        elements:
+        - class: File
+          identifier: forward
+          path: https://zenodo.org/records/13710591/files/Pcov3_ITS2_S151_R1_001.fastq.gz
+        - class: File
+          identifier: reverse
+          path: https://zenodo.org/records/13710591/files/Pcov3_ITS2_S151_R2_001.fastq.gz
+  outputs:
+    Complete Output Zip:
+      path: test-data/Complete Output Zip.zip
+    OTU Table:
+      path: test-data/OTU Table.tabular
+    OTU fasta:
+      path: test-data/OTU fasta.fasta
+    OTU Phylogenetic Tree:
+      path: test-data/OTU Phylogenetic Tree.newick

topics/microbiome/tutorials/lotus2-identifying-fungi/workflows/lotus2-fungi-workflow.ga

@@ -0,0 +1,226 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Workflow for running LotuS2 tool on fungal ITS paired-end sequencing data, to identify the fungi present in the samples",
+    "comments": [],
+    "creator": [
+        {
+            "class": "Organization",
+            "name": "Society for the Protection of Underground Networks",
+            "url": "https://spun.earth"
+        },
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0001-5902-6641",
+            "name": "Sujai Kumar",
+            "url": "https://github.com/sujaikumar"
+        },
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0002-0137-6953",
+            "name": "Bethan Manley",
+            "url": "https://github.com/bethanmanley"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
+    "steps": {
+        "0": {
+            "annotation": "Mapping file needed by LotuS2 to link sample metadata to a pair of fastq files",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Mapping file needed by LotuS2 to link sample metadata to a pair of fastq files",
+                    "name": "Mapping tsv"
+                }
+            ],
+            "label": "Mapping tsv",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0.124267578125
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "1d2315cd-11dc-494f-9698-0749cc89bd98",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "1": {
+            "annotation": "SDM (sequence demultiplexer tool) options needed for fungal ITS illumina paired-end sequencing",
+            "content_id": null,
+            "errors": null,
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "SDM (sequence demultiplexer tool) options needed for fungal ITS illumina paired-end sequencing",
+                    "name": "sdm Options txt"
+                }
+            ],
+            "label": "sdm Options txt",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 120.124267578125
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "0a86f2eb-afa0-415a-9f61-496a68eb893d",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "2": {
+            "annotation": "List of paired fastq files needed to run LotuS2. These files MUST match the files in the Mapping File",
+            "content_id": null,
+            "errors": null,
+            "id": 2,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "List of paired fastq files needed to run LotuS2. These files MUST match the files in the Mapping File",
+                    "name": "Input Dataset Collection"
+                }
+            ],
+            "label": "Input Dataset Collection",
+            "name": "Input dataset collection",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 240.124267578125
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list:paired\"}",
+            "tool_version": null,
+            "type": "data_collection_input",
+            "uuid": "4177013a-2f92-4800-9a85-517b43c45aa2",
+            "when": null,
+            "workflow_outputs": []
+        },
+        "3": {
+            "annotation": "LotuS2 creates a large output folder which is zipped up and provided as one of the outputs. Some of the individual files within this output folder are also exposed as outputs by the Galaxy LotuS2 tool so that they can be used in subsequent downstream analyses.",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "inputs|pair_input": {
+                    "id": 2,
+                    "output_name": "output"
+                },
+                "map": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "other_opts|sdmopt": {
+                    "id": 1,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool LotuS2",
+                    "name": "inputs"
+                },
+                {
+                    "description": "runtime parameter for tool LotuS2",
+                    "name": "other_opts"
+                }
+            ],
+            "label": "LotuS2",
+            "name": "LotuS2",
+            "outputs": [
+                {
+                    "name": "outputs",
+                    "type": "zip"
+                },
+                {
+                    "name": "otu",
+                    "type": "tabular"
+                },
+                {
+                    "name": "otu_fna",
+                    "type": "fasta"
+                },
+                {
+                    "name": "OTUphylo_nwk",
+                    "type": "newick"
+                },
+                {
+                    "name": "mapping",
+                    "type": "tabular"
+                },
+                {
+                    "name": "runlog",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 220,
+                "top": 0
+            },
+            "post_job_actions": {
+                "ChangeDatatypeActionOTUphylo_nwk": {
+                    "action_arguments": {
+                        "newtype": "newick"
+                    },
+                    "action_type": "ChangeDatatypeAction",
+                    "output_name": "OTUphylo_nwk"
+                }
+            },
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/earlhaminst/lotus2/lotus2/2.32+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "eb7baf1f72ca",
+                "name": "lotus2",
+                "owner": "earlhaminst",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"__input_ext\": \"input\", \"aligner_cond\": {\"taxAligner\": \"2\", \"__current_case__\": 1, \"refDB_cond\": {\"refDB\": \"cached\", \"__current_case__\": 0, \"ref_db\": \"UNITE\", \"greengenesSpecies\": false}, \"useBestBlastHitOnly\": false}, \"chromInfo\": \"/opt/galaxy/tool-data/shared/ucsc/chrom/?.len\", \"clu_args\": {\"derepMin\": \"10:1,5:2,3:3\", \"deactivateChimeraCheck\": \"\", \"chim_skew\": null}, \"clu_cond\": {\"clustering\": \"8\", \"__current_case__\": 3}, \"forwardPrimer\": \"\", \"inputs\": {\"paired_or_single\": \"paired_collection\", \"__current_case__\": 1, \"pair_input\": {\"__class__\": \"ConnectedValue\"}}, \"map\": {\"__class__\": \"ConnectedValue\"}, \"other_opts\": {\"sdmopt\": {\"__class__\": \"ConnectedValue\"}, \"platform\": \"\", \"barcode\": null, \"offtarget_cond\": {\"offtargetDB\": \"no\", \"__current_case__\": 0}, \"useMini4map\": true}, \"reversePrimer\": \"\", \"tax_args\": {\"amplicon_cond\": {\"amplicon_type\": \"ITS2\", \"__current_case__\": 5, \"ITSx\": true}, \"tax_group\": \"fungi\", \"keepUnclassified\": true, \"LCA_cover\": null, \"LCA_frac\": null, \"lulu\": true, \"buildPhylo\": \"1\", \"taxExcludeGrep\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.32+galaxy0",
+            "type": "tool",
+            "uuid": "8d82af5f-993a-46dd-afc9-8b73170da85d",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "OTU Table",
+                    "output_name": "otu",
+                    "uuid": "7ff13687-fb95-4b54-8b5c-4c916500dfed"
+                },
+                {
+                    "label": "OTU fasta",
+                    "output_name": "otu_fna",
+                    "uuid": "b3413904-3319-4fa0-8c17-2c4757af5b8c"
+                },
+                {
+                    "label": "Complete Output Zip",
+                    "output_name": "outputs",
+                    "uuid": "11ad8056-9572-428a-a3b2-5ceec0fa186e"
+                },
+                {
+                    "label": "OTU Phylogenetic Tree",
+                    "output_name": "OTUphylo_nwk",
+                    "uuid": "21d55970-8b95-4dca-9b46-e7c65340ce84"
+                }
+            ]
+        }
+    },
+    "tags": [
+        "lotus2",
+        "fungi",
+        "ecology",
+        "metagenomics"
+    ],
+    "uuid": "7016b008-431d-4138-bae3-b0653d0e89ce",
+    "version": 10
+}