run_malt false in test and add text in output.md

conf/test.config

@@ -25,7 +25,7 @@ params {
     perform_shortread_qc                  = true
     perform_longread_qc                   = true
     shortread_qc_mergepairs               = true
-    perform_shortread_complexityfilter    = false
+    perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
     perform_longread_hostremoval          = true
     perform_runmerging                    = true
@@ -33,7 +33,7 @@ params {
     run_kaiju                             = true
     run_kraken2                           = true
     run_bracken                           = true
-    run_malt                              = true
+    run_malt                              = false
     run_metaphlan3                        = true
     run_centrifuge                        = true
     run_diamond                           = true

docs/output.md

@@ -463,6 +463,8 @@ The following report files are used for the taxpasta step:
 - MetaPhlAn3: `<sample_id>_profile.txt` Taxpasta uses the `relative_abundance` column multiplied with a fixed number to yield an integer for the standardised profile.
 - mOTUs: `<sample_id>.out` Taxpasta uses the `read_count` column for the standardised profile.
 
+Please aware the outputs of each tool's standardised profile _may not_ be directly comparable between each tool. Some may report raw read counts, whereas others may report abundance information. Please always refer to the list above, for which information is used for each tool.
+
 ### MultiQC
 
 <details markdown="1">

subworkflows/local/standardisation_profiles.nf

@@ -141,7 +141,6 @@ workflow STANDARDISATION_PROFILES {
     ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
     ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
 
-
     // mOTUs
 
     // mOTUs has a 'single' database, and cannot create custom ones.