From c924e2e25ab1e6a11944323d5dec9585e39a27af Mon Sep 17 00:00:00 2001
From: "Philip R. Kensche"
Date: Wed, 9 Feb 2022 12:07:57 +0100
Subject: [PATCH] Update release info. Added documentation for how to install
Singularity container.
---
README.md | 18 +++++++++++++++---
1 file changed, 15 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index a026a26..6761f2f 100644
--- a/README.md
+++ b/README.md
@@ -115,7 +115,6 @@ The following "environment" profiles that define which environment will be used
* mamba
* docker
* singularity
-* dkfzModules: This environment uses the environment modules available in the DKFZ Cluster.
Currently, there are only two "executor" profiles that define the job execution method. These are
* local: Just execute the jobs locally on the system that executes Nextflow.
@@ -125,7 +124,18 @@ Please refer to the [Nextflow documentation](https://www.nextflow.io/docs/latest
### Location of Environments
-By default the Conda environments of the jobs as well as the Singularity containers are stored in subdirectories of the `cache/` subdirectory of the workflows installation directory (a.k.a `projectDir` by Nextflow).
+By default the Conda environments of the jobs as well as the Singularity containers are stored in subdirectories of the `cache/` subdirectory of the workflows installation directory (a.k.a `projectDir` by Nextflow). E.g. to use the Singularity container you can install the container as follows
+
+```bash
+cd $workflowRepoDir
+# Refer to the nextflow.config for the name of the Singularity image.
+singularity build \
+ cache/singularity/nf-bam2fastq_1.0.0.sif \
+ docker-daemon://ghcr.io/dkfz-odcf/nf-bam2fastq:latest
+
+# Test your container
+test/test1.sh test-results/ singularity nextflowEnv/
+```
This is suited for either a user-specific installation or for a centralized installation for which the environments should be shared for all users. Please refer to the `nextflow.config` or the `NXF_*_CACHEDIR` environment variables to change this default (see [here](https://www.nextflow.io/docs/latest/config.html#environment-variables).
@@ -177,10 +187,12 @@ For all commits with a tag that follows the pattern `\d+\.\d+\.\d+` the job cont
## Release Notes
-* 1.1.0 (January, 2022)
+* 1.1.0 (February, 2022)
* Minor: Added `--publishMode` option to allow user to select the [Nextflow publish mode](https://www.nextflow.io/docs/latest/process.html#publishdir). Default: `rellink`. Note that the former default was `symlink`, but as this change is considered negligible we classified the change as "minor".
+ * Minor: Removed `dkfzModules` profile. Didn't work well and was originally only for development. Please use 'conda', 'singularity' or 'docker'. The container-based environments provide the best reproducibility.
* Patch: Switched from Travis to CircleCI for continuous integration.
+
* 1.0.1 (October 14., 2021)
* Patch: Fix memory calculation as exponential backoff
* Patch: Job names now contain workflow name and job/task hash. Run name seems currently not possible to include there (due to a possible bug in Nextflow).