diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index e4c5fe7..e17dafe 100644 --- a/.github/workflows/deploy.yml +++ b/.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 \ No newline at end of file diff --git a/README.md b/README.md index 0e2caab..0d3e94f 100644 --- a/README.md +++ b/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. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5ad8bf4..dafc087 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-mouse + This report has been generated by the sf-mouse analysis pipeline. report_section_order: diff --git a/assets/nf-mouse-dark-logo.png b/assets/sf-mouse-dark-logo.png similarity index 100% rename from assets/nf-mouse-dark-logo.png rename to assets/sf-mouse-dark-logo.png diff --git a/assets/nf-mouse-light-logo.png b/assets/sf-mouse-light-logo.png similarity index 100% rename from assets/nf-mouse-light-logo.png rename to assets/sf-mouse-light-logo.png diff --git a/conf/base.config b/conf/base.config index f869866..aeea44f 100644 --- a/conf/base.config +++ b/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 diff --git a/conf/test.config b/conf/test.config index f569b80..e68aebe 100644 --- a/conf/test.config +++ b/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, --outdir + nextflow run sf-mouse -profile test, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full.config b/conf/test_full.config index f0e4b70..9584732 100644 --- a/conf/test_full.config +++ b/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, --outdir + nextflow run sf-mouse -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/main.nf b/main.nf index 4d55601..081f618 100644 --- a/main.nf +++ b/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: $params.use_gpu") // Define channel for multiqc files ch_multiqc_files = Channel.empty() diff --git a/nextflow.config b/nextflow.config index d1a8d9a..f1b32a7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -789,7 +789,7 @@ dag { } manifest { - name = 'scilus/nf-mouse' + name = 'scilus/sf-mouse' contributors = [ [ name: 'Elise Cosenza', @@ -809,8 +809,8 @@ manifest { ], ] - homePage = 'https://github.com/scilus/nf-mouse' - description = """nf-mouse is a neuroimaging pipeline to process ex-vivo dMRI data.""" + homePage = 'https://github.com/scilus/sf-mouse' + description = """sf-mouse is a neuroimaging pipeline to process ex-vivo dMRI data.""" mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.10.0' diff --git a/nextflow_schema.json b/nextflow_schema.json index 1d8eece..2ba1afd 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,8 +1,8 @@ { "$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" }