Add singularity/apptainer warning

CHANGELOG.md

@@ -3,8 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 1.1.0dev - [date]
+## [1.0.1] - date
 
-## 1.0.0 - [2023-10-17]
+### Enhancements & fixes
+
+- [[PR #66](https://github.com/nf-core/pixelator/pull/66)] - Add a warning and workaround for singularity & apptainer
+
+## [1.0.0] - 2023-10-17
 
 Initial release of nf-core/pixelator.

README.md

@@ -27,6 +27,11 @@ It takes a samplesheet as input and will process your data using `pixelator` to
 7. Analyze the cells for polarization and colocalization ([`pixelator analysis`](https://github.com/PixelgenTechnologies/pixelator))
 8. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))
 
+> **Warning**
+> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
+> This causes issues in some dependencies. As a workaround, you can revert tot the old behavior by setting the environment variable
+> `NXF_APPTAINER_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.
+
 ## Usage
 
 :::note
@@ -86,7 +91,8 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-If you use  nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)
+
+If you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112)
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

docs/usage.md

@@ -239,6 +239,12 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
+:::warning
+Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
+This causes issues in some dependencies. As a workaround, you can revert tot the old behavior by setting the environment variable
+`NXF_APPTAINER_HOME_MOUNT` to `true` in the machine from which you launch the pipeline.
+:::
+
 ### `-resume`
 
 Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html).

nextflow.config

@@ -161,7 +161,6 @@ profiles {
     singularity {
         singularity.enabled    = true
         singularity.autoMounts = true
-        singularity.runOptions = '--writable-tmpfs'
         conda.enabled          = false
         docker.enabled         = false
         podman.enabled         = false
@@ -200,7 +199,6 @@ profiles {
     apptainer {
         apptainer.enabled      = true
         apptainer.autoMounts   = true
-        apptainer.runOptions   = '--writable-tmpfs'
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false