Sf mouse

.github/workflows/deploy.yml

@@ -12,14 +12,14 @@ on:
 jobs:
   build-only:
     if: github.event_name == 'pull_request_target'
-    uses: scilus/nf-mouse-documentation/.github/workflows/deploy.yml@main
+    uses: scilus/sf-mouse-documentation/.github/workflows/deploy.yml@main
     with:
       deploy: false
     secrets: inherit
 
   build-and-deploy:
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-    uses: scilus/nf-mouse-documentation/.github/workflows/deploy.yml@main
+    uses: scilus/sf-mouse-documentation/.github/workflows/deploy.yml@main
     with:
       deploy: true
     secrets: inherit

README.md

@@ -1,10 +1,10 @@
-![alt text](assets/nf-mouse-light-logo.png "nf-mouse")
+![alt text](assets/sf-mouse-light-logo.png "sf-mouse")
 
-# nf-mouse
+# sf-mouse
 
-nf-mouse pipeline is developed by the Sherbrooke Connectivity Imaging Lab (SCIL) and Neurofunctional Imaging Group (GIN-IMN) in order to process diffusion MRI dataset from the raw data to the tractography.
+sf-mouse pipeline is developed by the Sherbrooke Connectivity Imaging Lab (SCIL) and Neurofunctional Imaging Group (GIN-IMN) in order to process diffusion MRI dataset from the raw data to the tractography.
 
-Using on diffusion data nf-mouse is a nextflow pipeline based on [nf-neuro](https://github.com/scilus/nf-neuro).
+Using on diffusion data sf-mouse is a nextflow pipeline based on [nf-neuro](https://github.com/scilus/nf-neuro).
 
 It incorporates essential steps: denoising, corrections of some artefacts, registration to a template (Allen Mouse Brain Atlas), the DTI and QBall reconstructions, extraction of some metrics, until constructing a whole brain tractogram of the mouse brain and extracting some bundles. It is capable of adapting the resolution of the atlas according to the native data, for better anatomical alignment.
 

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/scilus/nf-mouse/" target="_blank">nf-mouse</a>
+  This report has been generated by the <a href="https://github.com/scilus/sf-mouse/" target="_blank">sf-mouse</a>
   analysis pipeline.
 
 report_section_order:

conf/base.config

@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    nf-nf-mouse Nextflow base config file
+    sf-mouse Nextflow base config file
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on

conf/test.config

@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-nf-mouse -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run sf-mouse -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

conf/test_full.config

@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-nf-mouse -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run sf-mouse -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

main.nf

@@ -57,7 +57,7 @@ workflow get_data {
 
 workflow {
 
-    log.warn('During the first execution, nf-mouse may take some time to download the necessary modules.')
+    log.warn('During the first execution, sf-mouse may take some time to download the necessary modules.')
     log.info("Uses GPU: $params.use_gpu")
     // Define channel for multiqc files
     ch_multiqc_files = Channel.empty()

nextflow.config

@@ -789,7 +789,7 @@ dag {
 }
 
 manifest {
-    name            = 'scilus/nf-mouse'
+    name            = 'scilus/sf-mouse'
     contributors    = [
         [
             name: 'Elise Cosenza',
@@ -809,8 +809,8 @@ manifest {
         ],
     ]
 
-    homePage        = 'https://github.com/scilus/nf-mouse'
-    description     = """nf-mouse is a neuroimaging pipeline to process ex-vivo dMRI data."""
+    homePage        = 'https://github.com/scilus/sf-mouse'
+    description     = """sf-mouse is a neuroimaging pipeline to process ex-vivo dMRI data."""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.10.0'

nextflow_schema.json

@@ -1,8 +1,8 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/scilus/nf-mouse/nextflow_schema.json",
-    "title": "scilus/nf-mouse pipeline parameters",
-    "description": "nf-mouse is a neuroimaging pipeline to process ex-vivo dMRI data.",
+    "$id": "https://raw.githubusercontent.com/scilus/sf-mouse/nextflow_schema.json",
+    "title": "scilus/sf-mouse pipeline parameters",
+    "description": "sf-mouse is a neuroimaging pipeline to process ex-vivo dMRI data.",
     "type": "object",
     "$defs": {
         "input_output_options": {
@@ -22,13 +22,13 @@
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "description": "Path to the input directory location.",
-                    "help_text": "Ensure the data structure is respected. For more information, see the [documentation](https://scilus.github.io/nf-mouse/guides/inputs/)",
+                    "help_text": "Ensure the data structure is respected. For more information, see the [documentation](https://scilus.github.io/sf-mouse/guides/inputs/)",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "outdir": {
                     "type": "string",
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
-                    "help_text": "For a detailed description of the output files, please see the [documentation](https://scilus.github.io/nf-mouse/guides/outputs/).",
+                    "help_text": "For a detailed description of the output files, please see the [documentation](https://scilus.github.io/sf-mouse/guides/outputs/).",
                     "fa_icon": "fas fa-folder-open",
                     "default": "results_mouse"
                 }