diff --git a/subworkflows/local/longread_hostremoval.nf b/subworkflows/local/longread_hostremoval.nf
index f9ad593..83660fe 100644
--- a/subworkflows/local/longread_hostremoval.nf
+++ b/subworkflows/local/longread_hostremoval.nf
@@ -45,8 +45,6 @@ workflow LONGREAD_HOSTREMOVAL {
     SAMTOOLS_INDEX ( MINIMAP2_ALIGN.out.bam )
     ch_versions      = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
 
-    // FIXME: This join is performed using entire maps as keys.
-    //  Please replace with joining on specific keys instead.
     bam_bai = MINIMAP2_ALIGN.out.bam
         .join(SAMTOOLS_INDEX.out.bai)
 
diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
index 4d89464..e9440b3 100644
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@@ -87,7 +87,6 @@ workflow PROFILING {
                     [ new_meta, reads, db ]
 
             }
-            // FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
             .groupTuple(by: [0,2])
             .multiMap {
                 meta, reads, db ->
@@ -321,7 +320,6 @@ workflow PROFILING {
                                         meta, reads, db_meta, db ->
                                             [[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
                                     }
-                                    // FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
                                     .groupTuple(by: [0,2,3])
                                     .multiMap {
                                         single_meta, reads, db_meta, db ->
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf
index 560d660..26355b7 100644
--- a/subworkflows/local/standardisation_profiles.nf
+++ b/subworkflows/local/standardisation_profiles.nf
@@ -30,7 +30,6 @@ workflow STANDARDISATION_PROFILES {
                                         meta_new.tool = meta.tool == 'metaphlan3' ? 'metaphlan' : meta.tool == 'malt' ? 'megan6' : meta.tool
                                         [meta_new, profile]
                             }
-                            // FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
                             .groupTuple ()
                             .map { [ it[0], it[1].flatten() ] }
 
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index fff52e4..e44015f 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -197,7 +197,6 @@ workflow TAXPROFILER {
                     meta_new.remove('run_accession')
                     [ meta_new, reads ]
             }
-            // FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
             .groupTuple()
             .map {
                 meta, reads ->