changed pipeline name from nf-core-resolvi to parallax

Author: ctastad

CHANGELOG.md

@@ -1,11 +1,11 @@
-# nf-core/resolvinf: Changelog
+# nf-core/parallax: Changelog
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## v1.0dev - [2025-06-06]
 
-Initial release of nf-core/resolvinf, created with the [nf-core](http://nf-co.re/) template.
+Initial release of nf-core/parallax, created with the [nf-core](http://nf-co.re/) template.
 
 ### `Added`
 

Dockerfile

@@ -1,16 +1,16 @@
 FROM nfcore/base:2.1
 LABEL authors="Christopher Tastad" \
-      description="Docker image containing all software requirements for the nf-core/resolvinf pipeline"
+      description="Docker image containing all software requirements for the nf-core/parallax pipeline"
 
 # Install the conda environment
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-resolvinf-1.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/parallax-1.0dev/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-resolvinf-1.0dev > nf-core-resolvinf-1.0dev.yml
+RUN conda env export --name parallax-1.0dev > parallax-1.0dev.yml
 
 # Install additional Python packages not available in conda
 RUN pip install --no-cache-dir \

README.md

@@ -1,17 +1,17 @@
-# ![nf-core/resolvinf](docs/images/nf-core-resolvinf_logo.png)
+# ![nf-core/parallax](docs/images/nf-core-parallax_logo.png)
 
 **A Nextflow implementation of ResolVI and scVIVA for comprehensive spatial transcriptomics analysis**.
 
-[![GitHub Actions CI Status](https://github.com/nf-core/resolvinf/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/resolvinf/actions)
-[![GitHub Actions Linting Status](https://github.com/nf-core/resolvinf/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/resolvinf/actions)
+[![GitHub Actions CI Status](https://github.com/nf-core/parallax/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/parallax/actions)
+[![GitHub Actions Linting Status](https://github.com/nf-core/parallax/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/parallax/actions)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A523.04.0-brightgreen.svg)](https://www.nextflow.io/)
 
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
-[![Docker](https://img.shields.io/docker/automated/nfcore/resolvinf.svg)](https://hub.docker.com/r/nfcore/resolvinf)
+[![Docker](https://img.shields.io/docker/automated/nfcore/parallax.svg)](https://hub.docker.com/r/nfcore/parallax)
 
 ## Introduction
 
-**nf-core/resolvinf** is a comprehensive bioinformatics pipeline that integrates **ResolVI** (Resolution of Variational Inference) and **scVIVA** (single-cell Variational Inference for Variational Analysis) for advanced spatial transcriptomics data analysis. This dual-method approach provides state-of-the-art noise correction, cell type prediction, and niche-aware differential expression analysis.
+**nf-core/parallax** is a comprehensive bioinformatics pipeline that integrates **ResolVI** (Resolution of Variational Inference) and **scVIVA** (single-cell Variational Inference for Variational Analysis) for advanced spatial transcriptomics data analysis. This dual-method approach provides state-of-the-art noise correction, cell type prediction, and niche-aware differential expression analysis.
 
 ### Key Technologies
 
@@ -59,7 +59,7 @@ This parallel architecture maximizes computational efficiency while providing co
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
    ```bash
-   nextflow run nf-core/resolvinf -profile test,docker --outdir <OUTDIR>
+   nextflow run nf-core/parallax -profile test,docker --outdir <OUTDIR>
    ```
 
    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -72,7 +72,7 @@ This parallel architecture maximizes computational efficiency while providing co
 4. Start running your own analysis!
 
    ```bash
-   nextflow run nf-core/resolvinf --input samplesheet.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+   nextflow run nf-core/parallax --input samplesheet.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
 ## Input Requirements
@@ -154,6 +154,7 @@ The scVIVA workflow supports flexible condition specifications for niche-aware d
 ### Condition Types
 
 #### 1. **Cell Type Comparisons** (Simple)
+
 Compare different cell types without specific conditions:
 
 ```json
@@ -167,6 +168,7 @@ Compare different cell types without specific conditions:
 ```
 
 #### 2. **Treatment/Disease Conditions**
+
 Compare the same cell type across different treatments or disease states:
 
 ```json
@@ -183,6 +185,7 @@ Compare the same cell type across different treatments or disease states:
 ```
 
 #### 3. **Spatial Region Conditions**
+
 Compare cell types or conditions across different spatial regions:
 
 ```json
@@ -199,6 +202,7 @@ Compare cell types or conditions across different spatial regions:
 ```
 
 #### 4. **Sample-Based Conditions**
+
 Map specific samples to conditions when metadata isn't directly encoded:
 
 ```json
@@ -217,6 +221,7 @@ Map specific samples to conditions when metadata isn't directly encoded:
 ```
 
 #### 5. **Cross-Condition Cell Type Comparisons**
+
 Compare different cell types across different conditions:
 
 ```json
@@ -236,37 +241,40 @@ Compare different cell types across different conditions:
 
 The pipeline automatically detects and establishes conditions using the following priority order:
 
-1. **Explicit condition column**: Uses the column specified in ```condition_column```
-2. **Sample mapping**: Creates conditions from ```samples_condition1``` and ```samples_condition2``` lists
-3. **Spatial regions**: Uses ```spatial_region``` column if available
-4. **Common metadata columns**: Automatically detects ```treatment```, ```tissue_type```, etc.
-5. **Sample ID fallback**: Uses ```sample_id``` as conditions if no other method works
+1. **Explicit condition column**: Uses the column specified in `condition_column`
+2. **Sample mapping**: Creates conditions from `samples_condition1` and `samples_condition2` lists
+3. **Spatial regions**: Uses `spatial_region` column if available
+4. **Common metadata columns**: Automatically detects `treatment`, `tissue_type`, etc.
+5. **Sample ID fallback**: Uses `sample_id` as conditions if no other method works
 
 ### Required Data Preparation
 
 Ensure your AnnData objects contain the necessary metadata:
 
 #### Essential Columns
-- **Cell type predictions**: ```resolvi_predicted``` (automatically generated by ResolVI)
-- **Sample information**: ```sample_id``` (automatically added during preprocessing)
+
+- **Cell type predictions**: `resolvi_predicted` (automatically generated by ResolVI)
+- **Sample information**: `sample_id` (automatically added during preprocessing)
 
 #### Optional Condition Columns
-- ```condition```: General condition labels
-- ```treatment```: Treatment/control labels  
-- ```tissue_type```: Tissue or disease state labels
-- ```spatial_region```: Spatial region annotations
-- ```timepoint```: Temporal conditions
+
+- `condition`: General condition labels
+- `treatment`: Treatment/control labels
+- `tissue_type`: Tissue or disease state labels
+- `spatial_region`: Spatial region annotations
+- `timepoint`: Temporal conditions
 - Custom condition columns as specified in your comparisons
 
 ### File Formats
 
 #### JSON Format (Recommended)
+
 ```json
 [
   {
     "name": "comparison_name",
     "group1": "Cell_Type_1",
-    "group2": "Cell_Type_2", 
+    "group2": "Cell_Type_2",
     "condition1": "condition_A",
     "condition2": "condition_B",
     "condition_column": "metadata_column",
@@ -277,6 +285,7 @@ Ensure your AnnData objects contain the necessary metadata:
 ```
 
 #### CSV Format
+
 ```csv
 name,group1,group2,condition1,condition2,condition_column
 tcells_vs_bcells,T cells,B cells,,,
@@ -286,16 +295,18 @@ treated_vs_control_tcells,T cells,T cells,treated,control,treatment
 ### Usage Examples
 
 #### Basic cell type comparison:
+
 ```bash
-nextflow run nf-core/resolvinf \
+nextflow run nf-core/parallax \
   --input samplesheet.csv \
   --scviva_comparisons simple_comparisons.json \
   --outdir results
 ```
 
 #### Complex condition-based analysis:
+
 ```bash
-nextflow run nf-core/resolvinf \
+nextflow run nf-core/parallax \
   --input samplesheet.csv \
   --scviva_comparisons complex_comparisons.json \
   --annotation_label cell_type \
@@ -313,18 +324,20 @@ nextflow run nf-core/resolvinf \
 ### Troubleshooting
 
 #### Common Issues:
+
 - **"Cannot establish conditions"**: Check that specified condition columns exist in your data
 - **"Insufficient cells"**: Reduce the number of comparisons or combine similar conditions
-- **"Sample not found"**: Verify sample IDs in ```samples_condition1/2``` match your data exactly
+- **"Sample not found"**: Verify sample IDs in `samples_condition1/2` match your data exactly
 
 #### Debug Information:
+
 The pipeline logs detailed information about:
+
 - Available metadata columns
 - Condition establishment methods used
 - Cell counts for each comparison group
 - Success/failure status for each comparison
 
-
 ## Key Parameters
 
 ### Core ResolVI Parameters
@@ -419,7 +432,7 @@ Ensure your execution environment has appropriate GPU drivers and CUDA support w
 
 ## Documentation
 
-The nf-core/resolvinf pipeline comes with documentation about the pipeline:
+The nf-core/parallax pipeline comes with documentation about the pipeline:
 
 1. [Installation](https://nf-co.re/usage/installation)
 2. Pipeline configuration
@@ -460,7 +473,7 @@ The combination of ResolVI and scVIVA provides:
 
 ## Credits
 
-nf-core/resolvinf was originally written by Christopher Tastad.
+nf-core/parallax was originally written by Christopher Tastad.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -473,16 +486,16 @@ We thank the following people for their extensive assistance in the development
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-For further information or help, don't hesitate to get in touch on the [Slack `#resolvinf` channel](https://nfcore.slack.com/channels/resolvinf) (you can join with [this invite](https://nf-co.re/join/slack)).
+For further information or help, don't hesitate to get in touch on the [Slack `#parallax` channel](https://nfcore.slack.com/channels/parallax) (you can join with [this invite](https://nf-co.re/join/slack)).
 
 ## Citations
 
-If you use nf-core/resolvinf for your analysis, please cite:
+If you use nf-core/parallax for your analysis, please cite:
 
 ### Pipeline
 
 <!-- TODO: Add DOI after first release -->
-<!-- > **nf-core/resolvinf: A Nextflow implementation of ResolVI and scVIVA for comprehensive spatial transcriptomics analysis**
+<!-- > **nf-core/parallax: A Nextflow implementation of ResolVI and scVIVA for comprehensive spatial transcriptomics analysis**
 >
 > Christopher Tastad et al.
 >

assets/email_template.html

@@ -1,54 +1,71 @@
 <html>
+
 <head>
-  <head>
-  <meta charset="utf-8">
-  <meta http-equiv="X-UA-Compatible" content="IE=edge">
-  <meta name="viewport" content="width=device-width, initial-scale=1">
-
-  <meta name="description" content="nf-core/resolvinf: A Nextflow implementation of ResolVI for 10x Xenium data">
-  <title>nf-core/resolvinf Pipeline Report</title>
-</head>
+
+    <head>
+        <meta charset="utf-8">
+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
+        <meta name="viewport" content="width=device-width, initial-scale=1">
+
+        <meta name="description"
+            content="nf-core/parallax: A Nextflow implementation of downstream analysis for 10x Xenium data">
+        <title>nf-core/parallax Pipeline Report</title>
+    </head>
+
 <body>
-<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
+    <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
 
-<img src="cid:nfcorepipelinelogo">
+        <img src="cid:nfcorepipelinelogo">
 
-<h1>nf-core/resolvinf v${version}</h1>
-<h2>Run Name: $runName</h2>
+        <h1>nf-core/parallax v${version}</h1>
+        <h2>Run Name: $runName</h2>
 
-<% if (!success){
-    out << """
-    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        <h4 style="margin-top:0; color: inherit;">nf-core/resolvinf execution completed unsuccessfully!</h4>
-        <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
-        <p>The full error message was:</p>
-        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+        <% if (!success){ out << """
+    <div style=" color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px;
+            border: 1px solid transparent; border-radius: 4px;">
+            <h4 style="margin-top:0; color: inherit;">nf-core/parallax execution completed unsuccessfully!</h4>
+            <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
+            <p>The full error message was:</p>
+            <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
     </div>
     """
-} else {
+    } else {
     out << """
-    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
-        nf-core/resolvinf execution completed successfully!
-    </div>
-    """
-}
-%>
+    <div style=" color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px;
+        border: 1px solid transparent; border-radius: 4px;">
+        nf-core/parallax execution completed successfully!
+        </div>
+        """
+        }
+        %>
 
-<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
-<p>The command used to launch the workflow was as follows:</p>
-<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
+        <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+        <p>The command used to launch the workflow was as follows:</p>
+        <pre
+            style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">
+            $commandLine</pre>
 
-<h3>Pipeline Configuration:</h3>
-<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
-    <tbody style="border-bottom: 1px solid #ddd;">
-        <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
-    </tbody>
-</table>
+        <h3>Pipeline Configuration:</h3>
+        <table
+            style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
+            <tbody style="border-bottom: 1px solid #ddd;">
+                <% out << summary.collect{ k,v -> "<tr>
+                        <th
+                            style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>
+                            $k</th>
+                        <td
+                            style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>
+                            <pre style='white-space: pre-wrap; overflow: visible;'>$v</pre>
+                        </td>
+                    </tr>" }.join("\n") %>
+            </tbody>
+        </table>
 
-<p>nf-core/resolvinf</p>
-<p><a href="https://github.com/nf-core/resolvinf">https://github.com/nf-core/resolvinf</a></p>
+        <p>nf-core/parallax</p>
+        <p><a href="https://github.com/nf-core/parallax">https://github.com/nf-core/parallax</a></p>
 
-</div>
+        </div>
 
 </body>
+
 </html>

assets/email_template.txt

@@ -4,16 +4,16 @@
   |\\ | |__  __ /  ` /  \\ |__) |__         }  {
   | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
                                         `._,._,'
-  nf-core/resolvinf v${version}
+  nf-core/parallax v${version}
 ----------------------------------------------------
 
 Run Name: $runName
 
 <% if (success){
-    out << "## nf-core/resolvinf execution completed successfully! ##"
+    out << "## nf-core/parallax execution completed successfully! ##"
 } else {
     out << """####################################################
-## nf-core/resolvinf execution completed unsuccessfully! ##
+## nf-core/parallax execution completed unsuccessfully! ##
 ####################################################
 The exit status of the task that caused the workflow execution to fail was: $exitStatus.
 The full error message was:
@@ -36,5 +36,5 @@ Pipeline Configuration:
 <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
 
 --
-nf-core/resolvinf
-https://github.com/nf-core/resolvinf
+nf-core/parallax
+https://github.com/nf-core/parallax