Add SameStr workflow#1257
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Pull request overview
This PR adds a new microbiome workflow repository entry for running SameStr-based strain sharing detection on shotgun metagenomic reads, including documentation, Dockstore metadata, and a Planemo test definition.
Changes:
- Added the Galaxy workflow definition for SameStr with optional MetaPhlAn and mOTUs subworkflows.
- Added a Planemo test YAML plus Dockstore metadata for publishing/testing.
- Added initial README and CHANGELOG for the new workflow folder.
Reviewed changes
Copilot reviewed 4 out of 5 changed files in this pull request and generated 10 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/microbiome/samestr-workflow/Galaxy-Workflow-SameStr_Workflow.ga | New Galaxy workflow definition (SameStr + optional MetaPhlAn/mOTUs paths). |
| workflows/microbiome/samestr-workflow/Galaxy-Workflow-SameStr_Workflow-tests.yml | New Planemo test definition for the workflow (currently uses non-portable dataset references). |
| workflows/microbiome/samestr-workflow/.dockstore.yml | Dockstore descriptor pointing to the workflow and test files (missing ORCIDs). |
| workflows/microbiome/samestr-workflow/README.md | Workflow documentation (currently FMT-specific and outputs description doesn’t match workflow outputs). |
| workflows/microbiome/samestr-workflow/CHANGELOG.md | Initial changelog entry for first release. |
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| ## Inputs | ||
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| - **Raw Reads**: A collection of paired-end FASTQ files (`.fastq.gz`) representing pre-FMT, donor, and post-FMT samples |
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| ## Outputs | ||
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| - **stats_file**: Summary statistics of SNV profiles per sample | ||
| - **taxon_counts**: Taxonomic abundance table | ||
| - **strain_events**: Strain-level events detected across samples | ||
| - **cooccurrences**: Strain co-occurrence patterns across samples |
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| "outputs": [ | ||
| { | ||
| "label": "stats_file_metaphlan", | ||
| "output_name": "stats_file_metaphlan" | ||
| }, |
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| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "tool_state": "{\"alignment\": {\"alignment_tool\": {\"tool_choice\": \"bowtie2\", \"__current_case__\": 0, \"bowtie2_db\": \"hg19\"}, \"save_contaminants\": false}, \"fastqc\": {\"fastqc_report\": {\"select_fastqc\": \"no_fastqc\", \"__current_case__\": 1}, \"run_trim_repetitive\": false}, \"log_level\": \"INFO\", \"read_type\": {\"select_read_type\": \"paired\", \"__current_case__\": 1, \"save_unmatched\": true, \"paired_collection\": {\"__class__\": \"ConnectedValue\"}}, \"tandem\": {\"trf_step\": {\"trf_bool\": \"skip\", \"__current_case__\": 1}}, \"trimmomatic\": {\"trimmomatic_step\": {\"decide_trimmomatic\": \"run_trimmomatic\", \"__current_case__\": 0, \"sequencer\": \"NexteraPE\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", | ||
| "tool_uuid": null, | ||
| "tool_version": "0.12.1+galaxy1", |
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| authors: | ||
| - name: 'Xenia ' | ||
| familyName: "Morera Mart\xEDnez" | ||
| - name: 'Saim ' | ||
| familyName: Momin |
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| subclass: Galaxy | ||
| publish: true | ||
| primaryDescriptorPath: /Galaxy-Workflow-SameStr_Workflow.ga | ||
| testParameterFiles: | ||
| - /Galaxy-Workflow-SameStr_Workflow-tests.yml |
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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mvdbeek
reviewed
Jun 23, 2026
| testParameterFiles: | ||
| - /samestr-workflow-tests.yml | ||
| authors: | ||
| - name: 'Xenia Morera Martinez' |
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Can you please put your ORCID id here ?
mvdbeek
reviewed
Jun 23, 2026
| "name": "Xenia " | ||
| }, | ||
| { | ||
| "class": "Person", |
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this doesn't match the authors in .dockstore.yml, but please also add the orcid ids here
mvdbeek
reviewed
Jun 23, 2026
| "owner": "iuc", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "tool_state": "{\"alignment\": {\"alignment_tool\": {\"tool_choice\": \"bowtie2\", \"__current_case__\": 0, \"bowtie2_db\": \"hg19\"}, \"save_contaminants\": false}, \"fastqc\": {\"fastqc_report\": {\"select_fastqc\": \"no_fastqc\", \"__current_case__\": 1}, \"run_trim_repetitive\": false}, \"log_level\": \"INFO\", \"read_type\": {\"select_read_type\": \"paired\", \"__current_case__\": 1, \"save_unmatched\": true, \"paired_collection\": {\"__class__\": \"ConnectedValue\"}}, \"tandem\": {\"trf_step\": {\"trf_bool\": \"skip\", \"__current_case__\": 1}}, \"trimmomatic\": {\"trimmomatic_step\": {\"decide_trimmomatic\": \"run_trimmomatic\", \"__current_case__\": 0, \"sequencer\": \"NexteraPE\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", |
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Can you please make the bowtie database configurable ?
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It also seems like sequencer is something to make configurable ?
mvdbeek
reviewed
Jun 23, 2026
| This workflow processes paired-end shotgun metagenomic sequencing reads from multiple samples. It performs the following steps: | ||
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| - **Preprocessing**: Quality trimming and host read removal using KneadData | ||
| - **Taxonomic profiling**: MetaPhlAn4 or mOTUs for taxonomic classification |
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Is this different from Metaphlan below ?
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No, it's the same step. I'll add them together
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| "name": "kneaddata", | ||
| "owner": "iuc", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "tool_state": "{\"alignment\": {\"alignment_tool\": {\"tool_choice\": \"bowtie2\", \"__current_case__\": 0, \"bowtie2_db\": \"hg19\"}, \"save_contaminants\": false}, \"fastqc\": {\"fastqc_report\": {\"select_fastqc\": \"no_fastqc\", \"__current_case__\": 1}, \"run_trim_repetitive\": false}, \"log_level\": \"INFO\", \"read_type\": {\"select_read_type\": \"paired\", \"__current_case__\": 1, \"save_unmatched\": true, \"paired_collection\": {\"__class__\": \"ConnectedValue\"}}, \"tandem\": {\"trf_step\": {\"trf_bool\": \"skip\", \"__current_case__\": 1}}, \"trimmomatic\": {\"trimmomatic_step\": {\"decide_trimmomatic\": \"run_trimmomatic\", \"__current_case__\": 0, \"sequencer\": \"NexteraPE\"}}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", |
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| "name": "metaphlan", | ||
| "owner": "iuc", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "tool_state": "{\"analysis\": {\"analysis_type\": {\"t\": \"rel_ab\", \"__current_case__\": 0, \"tax_lev\": {\"tax_lev\": \"a\", \"__current_case__\": 0, \"split_levels\": false}}, \"min_alignment_len\": null, \"organism_profiling\": null, \"stat\": \"tavg_g\", \"stat_q\": \"0.2\", \"perc_nonzero\": \"0.33\", \"ignore_markers\": {\"__class__\": \"RuntimeValue\"}, \"avoid_disqm\": true}, \"inputs\": {\"in\": {\"selector\": \"raw\", \"__current_case__\": 0, \"raw_in\": {\"selector\": \"paired_collection\", \"__current_case__\": 2, \"in\": {\"__class__\": \"ConnectedValue\"}}, \"read_min_len\": \"70\", \"mapping\": {\"bt2_ps\": \"very-sensitive\", \"min_mapq_val\": \"5\"}}, \"db\": {\"db_selector\": \"cached\", \"__current_case__\": 0, \"cached_db\": \"mpa_vJan25_CHOCOPhlAnSGB_202503-11062025\", \"viral_analysis\": {\"profile_vsc\": \"\", \"__current_case__\": 1}}}, \"out\": {\"sample_id_key\": \"SampleID\", \"sample_id\": \"Metaphlan_Analysis\", \"use_group_representative\": false, \"CAMI_format_output\": false, \"skip_unclassified_estimation\": false, \"biom_format_output\": false, \"krona_output\": false}, \"subsample\": {\"selector\": \"no\", \"__current_case__\": 0}, \"test\": \"false\", \"__page__\": 0, \"__rerun_remap_job_id__\": null}", |
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| { | ||
| "class": "Person", | ||
| "familyName": "Morera Mart\u00ednez", | ||
| "name": "Xenia " | ||
| }, |
| "owner": "bgruening", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
| }, | ||
| "tool_state": "{\"algorithm_advanced_options\": {\"advanced_options\": {\"customize_algorithm_options\": \"default_options\", \"__current_case__\": 1}}, \"all_taxonomic_level\": false, \"biom_format\": false, \"cami_format_option\": {\"cami_options\": \"no\", \"__current_case__\": 1}, \"full_rank_taxonomy\": false, \"full_species_name\": false, \"inputs\": {\"input_type\": {\"selector\": \"reads\", \"__current_case__\": 0, \"reads_type\": {\"selector\": \"paired\", \"__current_case__\": 0, \"forward_reads\": {\"__class__\": \"ConnectedValue\"}, \"reverse_reads\": {\"__class__\": \"ConnectedValue\"}}}, \"sample_name\": null, \"db\": {\"db_source\": \"cached\", \"__current_case__\": 0, \"db_cached\": \"db_from_2026-04-27T094930Z\"}}, \"ncbi_taxonomy_ids\": false, \"ref_motus\": false, \"result_as_counts\": false, \"save_bam\": false, \"save_mgc\": false, \"taxonomic_level_option\": {\"taxonomic_option\": \"no\", \"__current_case__\": 1}, \"__page__\": 0, \"__rerun_remap_job_id__\": null}", |
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This one too should be configurable
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Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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@mvdbeek Thanks for the suggestions. I added the fixes, let me know if there's anything else that needs to be modified |
Member
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I see you've made the parameters runtime values, but can you please make them workflow input parameters ? Here's a tutorial that hopefully covers how to do this: https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-parameters/tutorial.html |
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@mvdbeek Thanks for the tutorial, it was very helpful. I'm not sure if it's now correct, I've added the parameters as text inputs in both the subworkflows and workflow. |
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I'm not sure why the test is failing, in the terminal both lint and test pass. I think it might be related to the subworkflows. @mvdbeek could you provide some insight on how to fix this? |
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Most of the databases and database values that the workflow uses are only available at usegalaxy.eu and are not portable to other Galaxy instances. We load the distributed CVMFS file system in the tests so that anyone can use these workflows. I'll see that we can sync these but that will take a couple of days. I would also strongly suggest using this for all databases instead of pre-specifying the valid options: |
Author
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Thanks @mvdbeek ! I’ve updated the database option. Let me know if any further fixes are needed from my side. |
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Author
Do we have any updates on this? |
Member
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working on that here: galaxyproject/idc#89. |
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FOR CONTRIBUTOR:
FOR REVIEWERS:
This workflow does/runs/performs … xyz … to generate/analyze/etc …namefield should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id