update output.md

nf-core · Oct 15, 2024 · 946ebb6 · 946ebb6
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diff --git a/docs/output.md b/docs/output.md
@@ -762,7 +762,7 @@ pipelines:
 
 </details>
 
-This pipeline only generates the `samplesheet` and `matrix` inputs. You will need to manually prepare the `contrast` table before running `nf-core/differentialabundance`.
+To generate the downsteam samplesheets for `nf-core/differentialabundance`, you need to turn on `--run_profile_standardisation`. The pipeline only generates the `samplesheet` and `matrix` inputs. You will need to manually prepare the `contrast` table before running `nf-core/differentialabundance`.
 
 `samplesheet.csv` includes sample IDs from the `taxpasta` output for each classifier. You will need to specify the conditions (the groups you want to compare) as desired.
 

diff --git a/subworkflows/local/generate_downstream_samplesheet/main.nf b/subworkflows/local/generate_downstream_samplesheet/main.nf
@@ -35,7 +35,7 @@ workflow GENERATE_DOWNSTREAM_SAMPLESHEETS {
     def downstreampipeline_names = params.generate_pipeline_samplesheets.split(",")
 
     if ( downstreampipeline_names.contains('differentialabundance')) {
-        SAMPLESHEET_TAXPROFILER(ch_databases)
+        SAMPLESHEET_DIFFERENTIALABUNDANCE(ch_taxpasta)
     }
 }