Update to use tractoflow subworkflow

.devcontainer/devcontainer.json

@@ -3,7 +3,15 @@
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
     "runArgs": ["--privileged"],
-
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+    },
+    "containerEnv": {
+        "NFCORE_MODULES_GIT_REMOTE": "https://github.com/scilus/nf-neuro.git",
+        "NFCORE_MODULES_BRANCH": "main",
+        "NFCORE_SUBWORKFLOWS_GIT_REMOTE": "https://github.com/scilus/nf-neuro.git",
+        "NFCORE_SUBWORKFLOWS_BRANCH": "main"
+    },
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.

.editorconfig

@@ -12,13 +12,27 @@ indent_style = space
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
+[modules/nf-core/**]
 charset = unset
 end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-[/subworkflows/nf-core/**]
+[subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
+# Same for nf-neuro
+[modules/nf-neuro/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+[subworkflows/nf-neuro/**]
 charset = unset
 end_of_line = unset
 insert_final_newline = unset

.github/workflows/ci.yml

@@ -24,7 +24,9 @@ jobs:
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'scilus/nf-tractoflow') }}"
     runs-on: ubuntu-latest
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
+      fail-fast: true
       matrix:
         NXF_VER:
           - "24.04.2"
@@ -37,6 +39,10 @@ jobs:
           - "test"
         isMaster:
           - ${{ github.base_ref == 'master' }}
+        include:
+          - experimental: false
+          - experimental: true
+            NXF_VER: "latest-everything"
         # Exclude conda and singularity on dev
         exclude:
           - isMaster: false

.gitignore

@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+node_modules/
+venv/

.nf-core.yml

@@ -8,6 +8,7 @@ lint:
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - conf/igenomes.config
+    - conf/igenomes_ignored.config
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-tractoflow_logo_light.png
@@ -19,6 +20,9 @@ lint:
   nextflow_config:
     - manifest.name
     - manifest.homePage
+  schema_lint: false
+  schema_params: false
+  schema_description: false
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:

.prettierignore

@@ -1,5 +1,6 @@
 email_template.html
 adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/

README.md

@@ -53,7 +53,7 @@ Now, you can run the pipeline using:
 ```bash
 nextflow run scilus/nf-tractoflow \
    -profile <docker/singularity/.../institute> \
-   --input samplesheet.csv \
+   <--input|--bids> samplesheet.csv \
    --outdir <OUTDIR>
 ```
 

assets/adaptivecard.json

@@ -5,7 +5,7 @@
             "contentType": "application/vnd.microsoft.card.adaptive",
             "contentUrl": null,
             "content": {
-                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                "$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
                 "msteams": {
                     "width": "Full"
                 },
@@ -50,12 +50,11 @@
                         "title": "Pipeline Configuration",
                         "card": {
                             "type": "AdaptiveCard",
-                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                            "$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
                             "body": [
                                 {
                                     "type": "FactSet",
-                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
-                                    ]
+                                    "facts": []
                                 }
                             ]
                         }

assets/methods_description_template.yml

@@ -3,20 +3,17 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "scilus/nf-tractoflow Methods Description"
 section_href: "https://github.com/scilus/nf-tractoflow"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using scilus/nf-tractoflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using scilus/nf-tractoflow v${workflow.manifest.version} ${doi_text} of the nf-neuro collection of workflows, part of nf-core (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
   <p>${tool_citations}</p>
   <h4>References</h4>
   <ul>
     <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
     <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
-    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
-    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    <li>Valcourt Caron, A., Boré, A., Edde, M., Gagnon, A., Thoumyre, S., Royer, A., Rheault, F., & Descoteaux, M. (2025). nf-neuro: developing maintainable pipelines for seamless processing of diffusion MRI. ISMRM 2025 Diffusion Workshop proceedings.</li>
     ${tool_bibliography}
   </ul>
   <div class="alert alert-info">

assets/samplesheet_raw.csv → assets/samplesheet.csv

@@ -1,4 +1,4 @@
-subject,dwi,bval,bvec,sbref,rev_dwi,rev_bval,rev_bvec,rev_sbref,t1,wmparc,aparc_aseg
-sub-01,/path/to/sub-01/dwi.nii.gz,/path/to/sub-01/dwi.bval,/path/to/sub-01/dwi.bvec,/path/to/sub-01/sbref.nii.gz,/path/to/sub-01/rev_dwi.nii.gz,/path/to/sub-01/rev_dwi.bval,/path/to/sub-01/rev_dwi.bvec,/path/to/sub-01/rev_sbref.nii.gz,/path/to/sub-01/t1.nii.gz,/path/to/sub-01/wmparc.nii.gz,/path/to/sub-01/aparc_aseg.nii.gz
-sub-02,/path/to/sub-02/dwi.nii.gz,/path/to/sub-02/dwi.bval,/path/to/sub-02/dwi.bvec,,,,,/path/to/sub-02/rev_sbref.nii.gz,/path/to/sub-02/t1.nii.gz,,
-sub-03,/path/to/sub-03/dwi.nii.gz,/path/to/sub-03/dwi.bval,/path/to/sub-03/dwi.bvec,,/path/to/sub-03/rev_dwi.nii.gz,/path/to/sub-03/rev_dwi.bval,/path/to/sub-03/rev_dwi.bvec,,/path/to/sub-03/t1.nii.gz,,
+subject,dwi,bval,bvec,sbref,rev_dwi,rev_bval,rev_bvec,rev_sbref,t1,wmparc,aparc_aseg,lesion
+sub-01,/path/to/sub-01/dwi.nii.gz,/path/to/sub-01/dwi.bval,/path/to/sub-01/dwi.bvec,/path/to/sub-01/sbref.nii.gz,/path/to/sub-01/rev_dwi.nii.gz,/path/to/sub-01/rev_dwi.bval,/path/to/sub-01/rev_dwi.bvec,/path/to/sub-01/rev_sbref.nii.gz,/path/to/sub-01/t1.nii.gz,/path/to/sub-01/wmparc.nii.gz,/path/to/sub-01/aparc_aseg.nii.gz,lesion.nii.gz
+sub-02,/path/to/sub-02/dwi.nii.gz,/path/to/sub-02/dwi.bval,/path/to/sub-02/dwi.bvec,,,,,/path/to/sub-02/rev_sbref.nii.gz,/path/to/sub-02/t1.nii.gz,,,
+sub-03,/path/to/sub-03/dwi.nii.gz,/path/to/sub-03/dwi.bval,/path/to/sub-03/dwi.bvec,,/path/to/sub-03/rev_dwi.nii.gz,/path/to/sub-03/rev_dwi.bval,/path/to/sub-03/rev_dwi.bvec,,/path/to/sub-03/t1.nii.gz,,,

assets/schema_raw_input.json → assets/schema_input.json

@@ -1,13 +1,13 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/AlexVCaron/nf-tractoflow/master/assets/schema_raw_input.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$id": "https://raw.githubusercontent.com/scilus/nf-tractoflow/master/assets/schema_input.json",
     "title": "nf-tractoflow pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",
     "items": {
         "type": "object",
         "minProperties": 5,
-        "maxProperties": 12,
+        "maxProperties": 13,
         "properties": {
             "subject": {
                 "type": "string",
@@ -179,6 +179,21 @@
                     }
                 ],
                 "errorMessage": "Segmentation of the cortical parcellation in Nifti format, cannot contain spaces and must have extension '.nii' or '.nii.gz'"
+            },
+            "lesion": {
+                "type": "string",
+                "anyOf": [
+                    {
+                        "format": "file-path",
+                        "exists": true,
+                        "pattern": "^\\S+(\\.nii)?\\.gz$"
+                    },
+                    {
+                        "format": "url",
+                        "mimetype": "application/gzip"
+                    }
+                ],
+                "errorMessage": "Lesion mask or map in Nifti format, cannot contain spaces and must have extension '.nii' or '.nii.gz'"
             }
         },
         "required": ["subject", "dwi", "bval", "bvec", "t1"]

assets/tests/raw_input_test.csv

@@ -1,2 +1,2 @@
 subject,dwi,bval,bvec,sbref,rev_dwi,rev_bval,rev_bvec,rev_sbref,t1,wmparc,aparc_aseg
-sub-test-1,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/2b/6f81ecdee186013956491fbda12e69,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/25/f1142227475e362e0381b42ec44433,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/ff/b5454f2212783f65e69b0fd7d242b1,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/09/442b32c4c459af4ba1b1628c6e2975,,,,,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/75/a767f8265ca41e497da70c97395057,,
+sub-test-1,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/2b/6f81ecdee186013956491fbda12e69,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/25/f1142227475e362e0381b42ec44433,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/ff/b5454f2212783f65e69b0fd7d242b1,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/09/442b32c4c459af4ba1b1628c6e2975,,,,,https://scil.usherbrooke.ca/scil_test_data/dvc-store/files/md5/75/a767f8265ca41e497da70c97395057,,,

conf/base.config

@@ -28,29 +28,29 @@ process {
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }
-        memory = { 6.GB * task.attempt }
+        memory = { 4.GB * task.attempt }
         time   = { 4.h  * task.attempt }
     }
     withLabel:process_low {
         cpus   = { 2     * task.attempt }
-        memory = { 12.GB * task.attempt }
+        memory = { 4.GB * task.attempt }
         time   = { 4.h   * task.attempt }
     }
     withLabel:process_medium {
         cpus   = { 6     * task.attempt }
-        memory = { 36.GB * task.attempt }
+        memory = { 8.GB * task.attempt }
         time   = { 8.h   * task.attempt }
     }
     withLabel:process_high {
         cpus   = { 12    * task.attempt }
-        memory = { 72.GB * task.attempt }
+        memory = { 12.GB * task.attempt }
         time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
         time   = { 20.h  * task.attempt }
     }
     withLabel:process_high_memory {
-        memory = { 200.GB * task.attempt }
+        memory = { 16.GB * task.attempt }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'