Update docs

Author: pinin4fjords

docs/usage.md

@@ -303,7 +303,7 @@ By default, the input GTF file will be filtered to ensure that sequence names co
 ## Contamination screening options
 
 :::note
-Not currently available using ARM architecture ('-profile arm')
+The `--contaminant_screening` option is not currently available using ARM architecture ('-profile arm')
 :::
 
 The pipeline provides the option to scan unaligned reads for contamination from other species using [Kraken2](https://ccb.jhu.edu/software/kraken2/), with the possibility of applying corrections from [Bracken](https://ccb.jhu.edu/software/bracken/). Since running Bracken is not computationally expensive, we recommend always using it to refine the abundance estimates generated by Kraken2.
@@ -364,6 +364,26 @@ genome: 'GRCh37'
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
+### Running on Linux ARM architectures
+
+The pipeline can be executed in an ARM compatible mode by specifying the ARM profile, for example:  
+
+```bash
+nextflow run \
+    nf-core/rnaseq \
+    --input <SAMPLESHEET> \
+    --outdir <OUTDIR> \
+    --gtf <GTF> \
+    --fasta <GENOME FASTA> \
+    -profile docker,arm
+```
+
+This will use ARM-compatible containers, and apply a small number of overrides to Conda definitions to support ARM operation. 
+
+:::warning
+Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability.
+:::
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
@@ -428,8 +448,13 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `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.
+- `arm`
   - A configuration profile that will set `docker.runOptions` appropriately for ARM architectures, and apply overrides supplying ARM-compatible containers and Conda environments.
 
+:::warning
+Please note that the ARM profile is experimental. It is expected to function correctly in all cases unless explicitly indicated otherwise—currently, exceptions include the use of the hisat2 aligner and contaminant screening via kraken2. However, because testing is presently conducted manually, we cannot guarantee its reliability.
+:::
+
 ### `-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).