diff --git a/CHANGELOG.md b/CHANGELOG.md
index d37f9758..b0e6cf2d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -57,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#150](https://github.com/nf-core/references/pull/150) - Replace `branch` with `filter` + `map` in datasheet_to_channel
 - [#151](https://github.com/nf-core/references/pull/151) - Enable static typing and replace `collectFile` with `WRITE_FILE`
 - [#153](https://github.com/nf-core/references/pull/153) - Update modules
+- [#156](https://github.com/nf-core/references/pull/156) - Replace legacy `groupTuple` and `transpose` operators with `groupBy` and `flatMap`
 
 ### Removed
 
diff --git a/main.nf b/main.nf
index a35da70f..160fa852 100644
--- a/main.nf
+++ b/main.nf
@@ -60,11 +60,11 @@ workflow NFCORE_REFERENCES {
 
     ncbi_download_input = fasta_download_input.to_download
         .mix(gff_download_input.to_download, gtf_download_input.to_download)
-        .map { meta, _file ->
-            [meta.source_version, meta.reference, meta]
-        }
-        .groupTuple()
-        .map { acc, ref_types, metas ->
+        .map { meta, _file -> [meta.source_version, [meta.reference, meta]] }
+        .groupBy()
+        .map { acc, entries ->
+            def ref_types = entries.collect { entry -> entry[0] }
+            def metas = entries.collect { entry -> entry[1] }
             def includes = ref_types
                 .collect { reference_ ->
                     reference_ == 'fasta'
diff --git a/subworkflows/local/datasheet_to_channel/main.nf b/subworkflows/local/datasheet_to_channel/main.nf
index e58910e5..7de33db7 100644
--- a/subworkflows/local/datasheet_to_channel/main.nf
+++ b/subworkflows/local/datasheet_to_channel/main.nf
@@ -151,7 +151,7 @@ workflow DATASHEET_TO_CHANNEL {
             known_snps,
             pon,
         )
-        .transpose()
+        .flatMap { meta, vcfs -> vcfs instanceof Path ? [[meta, vcfs]] : vcfs.toList().collect { vcf_ -> [meta, vcf_] } }
 
     emit:
     ascat_alleles    = ascat_alleles // channel: [meta, *.ascat_alleles.txt]
diff --git a/subworkflows/local/prepare_genome_rnaseq/main.nf b/subworkflows/local/prepare_genome_rnaseq/main.nf
index 9489c595..fea63d5d 100644
--- a/subworkflows/local/prepare_genome_rnaseq/main.nf
+++ b/subworkflows/local/prepare_genome_rnaseq/main.nf
@@ -39,7 +39,7 @@ workflow PREPARE_GENOME_RNASEQ {
 
     gtf = gtf
         .mix(GFFREAD.out.gtf)
-        .groupTuple()
+        .groupBy()
         .map { meta, gtf_ -> gtf_[1] ? [meta, gtf_[1]] : [meta, gtf_[0]] }
 
     HISAT2_EXTRACTSPLICESITES(gtf.filter { meta, _gtf -> ('hisat2' in tools || 'hisat2_extractsplicesites' in tools) && meta.run_hisat2 && !hisat2_skip_splice_sites })