Documentation updates

README.md

@@ -44,6 +44,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 RNA-seq:
 
+with deseq2:
 ```bash
  nextflow run nf-core/differentialabundance \
      --input samplesheet.csv \
@@ -54,6 +55,17 @@ RNA-seq:
      -profile rnaseq,<docker/singularity/podman/shifter/charliecloud/conda/institute>
 ```
 
+with limma+voom
+```bash
+ nextflow run nf-core/differentialabundance \
+     --input samplesheet.csv \
+     --contrasts contrasts.csv \
+     --matrix assay_matrix.tsv \
+     --gtf mouse.gtf \
+     --outdir <OUTDIR>  \
+     -profile rnaseq_limma,<docker/singularity/podman/shifter/charliecloud/conda/institute>
+```
+
 :::note
 If you are using the outputs of the nf-core rnaseq workflow as input here **either**:
 

docs/usage.md

@@ -307,7 +307,7 @@ The typical command for running the pipeline is as follows:
 
 ```bash
 nextflow run nf-core/differentialabundance \
-    [-profile rnaseq OR -profile affy] \
+    [-profile rnaseq OR -profile rnaseq_limma OR -profile affy] \
     --input samplesheet.csv \
     --contrasts contrasts.csv \
     [--matrix assay_matrix.tsv OR --affy_cel_files_archive cel_files.tar] \