diff --git a/conf/vsc_calcua.config b/conf/vsc_calcua.config
index b76387f5..37eef7da 100644
--- a/conf/vsc_calcua.config
+++ b/conf/vsc_calcua.config
@@ -13,13 +13,28 @@ cleanup = true
 // Check if APPTAINER_TMPDIR/SINGULARITY_TMPDIR environment variables are set.
 // If they are available, try to create the tmp directory at the specified location.
 // Skip if host is not CalcUA to avoid hindering github actions.
-if ( System.getenv("VSC_INSTITUTE") != "antwerpen" ) {
-    def apptainer_tmpdir = System.getenv("APPTAINER_TMPDIR") ?: System.getenv("SINGULARITY_TMPDIR") ?: null
-    if (! apptainer_tmpdir ) {
+
+// Check if environment variables for singularity/apptainer/nextflow cache and tmp dirs are set:
+// - APPTAINER_TMPDIR/SINGULARITY_TMPDIR,
+// - APPTAINER_CACHEDIR/SINGULARITY_CACHEDIR or
+// - NXF_APPTAINER_CACHEDIR/NXF_SINGULARITY_CACHEDIR
+// Define variables outside of conditional scope to make them usable elsewhere
+def apptainer_tmpdir = System.getenv("APPTAINER_TMPDIR") ?: System.getenv("SINGULARITY_TMPDIR") ?: null
+def apptainer_cachedir = System.getenv("APPTAINER_CACHEDIR") ?: System.getenv("SINGULARITY_CACHEDIR") ?: null
+def nxf_apptainer_cachedir = System.getenv("NXF_APPTAINER_CACHEDIR") ?: System.getenv("NXF_SINGULARITY_CACHEDIR") ?: null
+// Skip check if host is not CalcUA, to avoid hindering github actions.
+if ( System.getenv("VSC_INSTITUTE") == "antwerpen" ) {
+    // APPTAINER_TMPDIR/SINGULARITY_TMPDIR environment variable
+    if ( !apptainer_tmpdir ) {
         def tmp_dir = System.getenv("TMPDIR") ?: "/tmp"
         System.err.println("\nWARNING: APPTAINER_TMPDIR/SINGULARITY_TMPDIR environment variable was not found.\nPlease add the line 'export APPTAINER_TMPDIR=\"\${VSC_SCRATCH}/apptainer/tmp\"' to your ~/.bashrc file (or set it with sbatch or in your job script).\nDefaulting to local $tmp_dir on the execution node of the Nextflow head process.\n")
-        // TODO: check if images stored there can be accessed by slurm jobs on other nodes
     } else {
+        // if set, try to create the tmp directory at the specified location to avoid errors during
+        // docker image conversion (note that this only happens when no native singulariry/apptainer
+        // images are available):
+        //      FATAL:   While making image from oci registry: error fetching image to cache: while
+        //      building SIF from layers: unable to create new build: failed to create build parent dir:
+        //      stat /scratch/antwerpen/203/vsc20380/apptainer/tmp: no such file or directory
         apptainer_tmpdir = new File(apptainer_tmpdir)
         if (! apptainer_tmpdir.exists() ) {
             try {
@@ -29,6 +44,16 @@ if ( System.getenv("VSC_INSTITUTE") != "antwerpen" ) {
             }
         }
     }
+    // APPTAINER_CACHEDIR/SINGULARITY_CACHEDIR
+    if ( !apptainer_cachedir ) {
+        System.err.println("\nWARNING: APPTAINER_CACHEDIR/SINGULARITY_CACHEDIR environment variable was not found.\nPlease add the line 'export APPTAINER_CACHEDIR=\"\${VSC_SCRATCH}/apptainer/cache\"' to your ~/.bashrc file (or set it with sbatch or in your job script).\nUsing the default storage location of Singularity/Apptainer ~/.apptainer/cache/. Read more about why this should be avoided in the VSC docs: https://docs.vscentrum.be/software/singularity.html#building-on-vsc-infrastructure\n")
+        // TODO: optional exit out here.
+    }
+    // NXF_APPTAINER_CACHEDIR/NXF_SINGULARITY_CACHEDIR
+    if ( !nxf_apptainer_cachedir ) {
+        nxf_apptainer_cachedir = "$scratch_dir/apptainer/nextflow_cache"
+        System.err.println("\nWARNING: NXF_APPTAINER_CACHEDIR/NXF_SINGULARITY_CACHEDIR environment variable was not found.\nPlease add the line 'export NXF_APPTAINER_CACHEDIR=\"\${VSC_SCRATCH}/apptainer/nextflow_cache\"' to your ~/.bashrc file (or set it with sbatch or in your job script).\nDefaulting to $nxf_apptainer_cachedir instead of the nextflow work directory.\n")
+    }
 }
 
 // Function to check if the selected partition profile matches the partition on which the master
@@ -73,11 +98,10 @@ process {
 }
 
 // Specify that apptainer/singularity should be used and where the cache dir will be for the images.
-// The singularity directive is used in favour of the apptainer one, because currently the apptainer
+// Singularity is used in favour of apptainer, because currently the apptainer
 // variant will pull in (and convert) docker images, instead of using pre-built singularity ones.
-// To use the pre-built singularity containers instead, the singularity options should be selected
-// with apptainer installed on the system, which defines singularity as an alias (as is the case
-// on CalcUA).
+// On a system where singularity is defined as an alias for apptainer (as is the case on CalcUA),
+// this works out fine and results in pre-built singularity containers being downloaded.
 // See https://nf-co.re/docs/usage/installation#pipeline-software
 // and https://nf-co.re/tools#how-the-singularity-image-downloads-work
 // See https://www.nextflow.io/docs/latest/config.html#scope-singularity
@@ -85,7 +109,7 @@ singularity {
     enabled = true
     autoMounts = true
     // See https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
-    cacheDir = "$scratch_dir/apptainer/nextflow_cache"  // Equivalent to setting NXF_APPTAINER_CACHEDIR/NXF_SINGULARITY_CACHEDIR environment variable
+    cacheDir = "$nxf_apptainer_cachedir" // Equivalent to setting NXF_APPTAINER_CACHEDIR/NXF_SINGULARITY_CACHEDIR environment variable
 }
 
 // Define profiles for the following partitions:
diff --git a/docs/vsc_calcua.md b/docs/vsc_calcua.md
index 49a91608..1b37d34a 100644
--- a/docs/vsc_calcua.md
+++ b/docs/vsc_calcua.md
@@ -144,7 +144,7 @@ By default, Nextflow stores all of the intermediate files required to run the pi
 
 If the run does not complete successfully then the `work` directory should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH/work` per this configuration. You can also use the [`nextflow clean` command](https://www.nextflow.io/docs/latest/cli.html#clean) to clean up all files related to a specific run (including not just the `work` directory, but also log files and the `.nextflow` cache directory).
 
-> **NB:** The Nextflow `work` directory for any pipeline is located in `$VSC_SCRATCH` by default and is cleaned automatically after a success pipeline run, unless the `debug` profile is provided.
+> **NB:** The Nextflow `work` directory for any pipeline is located in `$VSC_SCRATCH/work` by default and is cleaned automatically after a success pipeline run, unless the `debug` profile is provided.
 
 ### Debug mode
 
@@ -233,14 +233,14 @@ The `nextflow run ...` command that launches the head process, can be invoked ei
 
 [Apptainer](https://apptainer.org/) is an open-source fork of [Singularity](https://sylabs.io/singularity/), which is an alternative container runtime to Docker. It is more suitable to usage on HPCs because it can be run without root privileges and does not use a dedicated daemon process. More info on the usage of Apptainer/Singularity on the VSC HPC can be found [here](https://docs.vscentrum.be/software/singularity.html).
 
-When executing Nextflow pipelines using Apptainer/Singularity, the container image files will by default be cached inside the pipeline work directory. The CalcUA config profile instead sets the [singularity.cacheDir setting](https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub) to a central location on your scratch space (`$VSC_SCRATCH/apptainer/nextflow_cache`), in order to reuse them between different pipelines. This is equivalent to setting the `NXF_APPTAINER_CACHEDIR`/`NXF_SINGULARITY_CACHEDIR` environment variables manually (but note that the `cacheDir` defined in the config file takes precedence and cannot be overwritten by setting the environment variable).
+When executing Nextflow pipelines using Apptainer/Singularity, the container image files will by default be cached inside the pipeline work directory (which for the `vsc_calcua` config would by default be set to `$VSC_SCRATCH/work`). The CalcUA config profile instead sets the [singularity.cacheDir setting](https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub) to a central location on your scratch space (`$VSC_SCRATCH/apptainer/nextflow_cache`), in order to reuse them between different pipelines even when cleaning the work directory. If the `NXF_APPTAINER_CACHEDIR`/`NXF_SINGULARITY_CACHEDIR` environment variables are set manually, they will take precedence over this default setting.
 
 Apptainer/Singularity makes use of two additional environment variables, `APPTAINER_CACHEDIR`/`SINGULARITY_CACHEDIR` and `APPTAINER_TMPDIR`/`SINGULARITY_TMPDIR`. As recommended by the [VSC documentation on containers](https://docs.vscentrum.be/software/singularity.html#building-on-vsc-infrastructure), these should be set to a location on the scratch system, to avoid exceeding the quota on your home directory file system.
 
 > **NB:** The cachedir and tmpdir are only used when new images are built or converted from existing docker images. For most nf-core pipelines this does not happen, since they will instead try to directly pull pre-built singularity images from [Galaxy Depot](https://depot.galaxyproject.org/singularity/)
 
-- The [cache directory](https://apptainer.org/docs/user/main/build_env.html#cache-folders) `APPTAINER_CACHEDIR`/`SINGULARITY_CACHEDIR` is used to store files and layers used during image creation (or conversion of Docker/OCI images). Its default location is `$HOME/.apptainer/cache`, but it is recommended to change this to `$VSC_SCRATCH/apptainer/cache` on the CalcUA HPC instead.
-- The [temporary directory](https://apptainer.org/docs/user/main/build_env.html#temporary-folders) `APPTAINER_TMPDIR`/`SINGULARITY_TMPDIR` is used to store temporary files when building an image (or converting a Docker/OCI source). The directory must have enough free space to hold the entire uncompressed image during all steps of the build process. Its default location is `/tmp`, but it is recommended to change this to `$VSC_SCRATCH/apptainer/tmp` on the CalcUA HPC instead. The reason being that the default `/tmp` would refer to a directory on the the compute node running the master nextflow process, which are [small SSDs on CalcUA](https://docs.vscentrum.be/antwerp/tier2_hardware/uantwerp_storage.html).
+- The [cache directory](https://apptainer.org/docs/user/main/build_env.html#cache-folders) `APPTAINER_CACHEDIR`/`SINGULARITY_CACHEDIR` is used to store files and layers used during image creation (or conversion of Docker/OCI images). Its default location is `$HOME/.apptainer/cache`, but we recommended changing it to `$VSC_SCRATCH/apptainer/cache` (or another location in scratch) on the CalcUA HPC instead, to avoid exceeding the quota in the home file system.
+- The [temporary directory](https://apptainer.org/docs/user/main/build_env.html#temporary-folders) `APPTAINER_TMPDIR`/`SINGULARITY_TMPDIR` is used to store temporary files when building an image (or converting a Docker/OCI source). The directory must have enough free space to hold the entire uncompressed image during all steps of the build process. Its default location is `/tmp` (or more accurately, `$TMPDIR` in the environment of the nextflow head process), but we recommended changing it to `$VSC_SCRATCH/apptainer/tmp` (or another location in scratch) on the CalcUA HPC instead. The reason being that the default `/tmp` would refer to a directory on the the compute node running the master nextflow process, which are [small SSDs on CalcUA](https://docs.vscentrum.be/antwerp/tier2_hardware/uantwerp_storage.html) that could get filled up.
 
   > **NB:** The tmp directory needs to be created manually beforehand, otherwise pipelines that need to pull in and convert docker images, or the manual building of images yourself, will fail.
 
@@ -252,7 +252,7 @@ These two variables can be set in several different ways:
 - Passed to `sbatch` as a parameter or on a `#SBATCH` line in the job script (e.g., `--export=APPTAINER_CACHEDIR=${VSC_SCRATCH}/apptainer/cache,APPTAINER_TMPDIR=${VSC_SCRATCH}/apptainer/tmp`).
 - Directly in your job script (e.g., `export APPTAINER_CACHEDIR=${VSC_SCRATCH}/apptainer/cache APPTAINER_TMPDIR=${VSC_SCRATCH}/apptainer/tmp`).
 
-However, note that for the `.bashrc` option to work, the environment need to be passed on to the slurm jobs. Currently, this seems to happen by default (i.e., variables defined in `~/.bashrc` are propagated), but there exist methods to enforce this more strictly. E.g., job scripts that start with `#!/bin/bash -l`, will ensure that jobs [launch using your login environment](https://docs.vscentrum.be/leuven/slurm_specifics.html#job-shell). Similarly, the `sbatch` options `[--get-user-env`](https://slurm.schedmd.com/sbatch.html#OPT_get-user-env) or [`--export=`](https://slurm.schedmd.com/sbatch.html#OPT_export) can be used. Also [see the CalcUA-specific](https://docs.vscentrum.be/jobs/slurm_pbs_comparison.html#main-differences-between-slurm-and-torque) and the [general VSC documentation for more info](https://docs.vscentrum.be/jobs/job_submission.html#the-job-environment).
+However, note that for the `.bashrc` option to work, the environment need to be passed on to the slurm jobs. Currently, this seems to happen by default (i.e., variables defined in `~/.bashrc` are propagated, as per [the VSC docs](https://docs.vscentrum.be/leuven/slurm_specifics.html#environment-propagation)), but there also exist methods to enforce this more strictly. E.g., job scripts that start with `#!/bin/bash -l`, will ensure that jobs [launch using your login environment](https://docs.vscentrum.be/leuven/slurm_specifics.html#job-shell). Similarly, the `sbatch` options [`--get-user-env`](https://slurm.schedmd.com/sbatch.html#OPT_get-user-env) or [`--export=`](https://slurm.schedmd.com/sbatch.html#OPT_export) can be used. Also [see the CalcUA-specific](https://docs.vscentrum.be/jobs/slurm_pbs_comparison.html#main-differences-between-slurm-and-torque) and the [general VSC documentation for more info](https://docs.vscentrum.be/jobs/job_submission.html#the-job-environment).
 
 Lastly, note that this config file currently uses the Singularity engine rather than the Apptainer one (see [`singularity` directive: `enabled = true`](https://www.nextflow.io/docs/latest/config.html#scope-singularity)). The reason is that, for the time being, using the apptainer engine in nf-core pipelines will result in docker images being pulled and converted to apptainer ones, rather than making use of pre-built singularity images (see [nf-core documentation](https://nf-co.re/docs/usage/installation#pipeline-software)). Conversely, when making use of the singularity engine, pre-built images are downloaded and Apptainer will still be used in the background for running these, since the installation of `apptainer` will by default create an alias for `singularity` (and this is also the case on CalcUA).