diff --git a/CHANGELOG.md b/CHANGELOG.md
index abab2aa9e..d910ab59b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
 - [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
 - [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
+- [PR #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
 - [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
 - [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability
 
diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov/main.nf
similarity index 100%
rename from modules/local/bedtools_genomecov.nf
rename to modules/local/bedtools_genomecov/main.nf
diff --git a/modules/local/cat_additional_fasta.nf b/modules/local/cat_additional_fasta/main.nf
similarity index 100%
rename from modules/local/cat_additional_fasta.nf
rename to modules/local/cat_additional_fasta/main.nf
diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc/main.nf
similarity index 100%
rename from modules/local/deseq2_qc.nf
rename to modules/local/deseq2_qc/main.nf
diff --git a/modules/local/dupradar.nf b/modules/local/dupradar/main.nf
similarity index 100%
rename from modules/local/dupradar.nf
rename to modules/local/dupradar/main.nf
diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed/main.nf
similarity index 100%
rename from modules/local/gtf2bed.nf
rename to modules/local/gtf2bed/main.nf
diff --git a/modules/local/gtf_gene_filter.nf b/modules/local/gtf_gene_filter/main.nf
similarity index 100%
rename from modules/local/gtf_gene_filter.nf
rename to modules/local/gtf_gene_filter/main.nf
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc/main.nf
similarity index 100%
rename from modules/local/multiqc.nf
rename to modules/local/multiqc/main.nf
diff --git a/modules/local/multiqc_custom_biotype.nf b/modules/local/multiqc_custom_biotype/main.nf
similarity index 100%
rename from modules/local/multiqc_custom_biotype.nf
rename to modules/local/multiqc_custom_biotype/main.nf
diff --git a/modules/local/preprocess_transcripts_fasta_gencode.nf b/modules/local/preprocess_transcripts_fasta_gencode/main.nf
similarity index 100%
rename from modules/local/preprocess_transcripts_fasta_gencode.nf
rename to modules/local/preprocess_transcripts_fasta_gencode/main.nf
diff --git a/modules/local/rsem_merge_counts.nf b/modules/local/rsem_merge_counts/main.nf
similarity index 100%
rename from modules/local/rsem_merge_counts.nf
rename to modules/local/rsem_merge_counts/main.nf
diff --git a/modules/local/salmon_summarizedexperiment.nf b/modules/local/salmon_summarizedexperiment/main.nf
similarity index 100%
rename from modules/local/salmon_summarizedexperiment.nf
rename to modules/local/salmon_summarizedexperiment/main.nf
diff --git a/modules/local/salmon_tx2gene.nf b/modules/local/salmon_tx2gene/main.nf
similarity index 100%
rename from modules/local/salmon_tx2gene.nf
rename to modules/local/salmon_tx2gene/main.nf
diff --git a/modules/local/salmon_tximport.nf b/modules/local/salmon_tximport/main.nf
similarity index 100%
rename from modules/local/salmon_tximport.nf
rename to modules/local/salmon_tximport/main.nf
diff --git a/modules/local/star_align_igenomes.nf b/modules/local/star_align_igenomes/main.nf
similarity index 100%
rename from modules/local/star_align_igenomes.nf
rename to modules/local/star_align_igenomes/main.nf
diff --git a/modules/local/star_genomegenerate_igenomes.nf b/modules/local/star_genomegenerate_igenomes/main.nf
similarity index 100%
rename from modules/local/star_genomegenerate_igenomes.nf
rename to modules/local/star_genomegenerate_igenomes/main.nf
diff --git a/modules/local/umitools_prepareforrsem.nf b/modules/local/umitools_prepareforrsem/main.nf
similarity index 100%
rename from modules/local/umitools_prepareforrsem.nf
rename to modules/local/umitools_prepareforrsem/main.nf
diff --git a/subworkflows/local/align_star.nf b/subworkflows/local/align_star/main.nf
similarity index 94%
rename from subworkflows/local/align_star.nf
rename to subworkflows/local/align_star/main.nf
index ffa027257..479ed2379 100644
--- a/subworkflows/local/align_star.nf
+++ b/subworkflows/local/align_star/main.nf
@@ -2,9 +2,9 @@
 // Alignment with STAR
 //
 
-include { STAR_ALIGN          } from '../../modules/nf-core/star/align/main'
-include { STAR_ALIGN_IGENOMES } from '../../modules/local/star_align_igenomes'
-include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main'
+include { STAR_ALIGN              } from '../../../modules/nf-core/star/align'
+include { STAR_ALIGN_IGENOMES     } from '../../../modules/local/star_align_igenomes'
+include { BAM_SORT_STATS_SAMTOOLS } from '../../nf-core/bam_sort_stats_samtools'
 
 workflow ALIGN_STAR {
     take:
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome/main.nf
similarity index 83%
rename from subworkflows/local/prepare_genome.nf
rename to subworkflows/local/prepare_genome/main.nf
index b83126cd7..200957cda 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -2,34 +2,34 @@
 // Uncompress and prepare reference genome files
 //
 
-include { GUNZIP as GUNZIP_FASTA            } from '../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_GTF              } from '../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_GFF              } from '../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_GENE_BED         } from '../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../modules/nf-core/gunzip/main'
-include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../modules/nf-core/gunzip/main'
+include { GUNZIP as GUNZIP_FASTA            } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_GTF              } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_GFF              } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_GENE_BED         } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip'
+include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip'
 
-include { UNTAR as UNTAR_BBSPLIT_INDEX      } from '../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_STAR_INDEX         } from '../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_RSEM_INDEX         } from '../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_HISAT2_INDEX       } from '../../modules/nf-core/untar/main'
-include { UNTAR as UNTAR_SALMON_INDEX       } from '../../modules/nf-core/untar/main'
+include { UNTAR as UNTAR_BBSPLIT_INDEX      } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_STAR_INDEX         } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_RSEM_INDEX         } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_HISAT2_INDEX       } from '../../../modules/nf-core/untar'
+include { UNTAR as UNTAR_SALMON_INDEX       } from '../../../modules/nf-core/untar'
 
-include { CUSTOM_GETCHROMSIZES              } from '../../modules/nf-core/custom/getchromsizes/main'
-include { GFFREAD                           } from '../../modules/nf-core/gffread/main'
-include { BBMAP_BBSPLIT                     } from '../../modules/nf-core/bbmap/bbsplit/main'
-include { STAR_GENOMEGENERATE               } from '../../modules/nf-core/star/genomegenerate/main'
-include { HISAT2_EXTRACTSPLICESITES         } from '../../modules/nf-core/hisat2/extractsplicesites/main'
-include { HISAT2_BUILD                      } from '../../modules/nf-core/hisat2/build/main'
-include { SALMON_INDEX                      } from '../../modules/nf-core/salmon/index/main'
-include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../modules/nf-core/rsem/preparereference/main'
-include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA       } from '../../modules/nf-core/rsem/preparereference/main'
+include { CUSTOM_GETCHROMSIZES              } from '../../../modules/nf-core/custom/getchromsizes'
+include { GFFREAD                           } from '../../../modules/nf-core/gffread'
+include { BBMAP_BBSPLIT                     } from '../../../modules/nf-core/bbmap/bbsplit'
+include { STAR_GENOMEGENERATE               } from '../../../modules/nf-core/star/genomegenerate'
+include { HISAT2_EXTRACTSPLICESITES         } from '../../../modules/nf-core/hisat2/extractsplicesites'
+include { HISAT2_BUILD                      } from '../../../modules/nf-core/hisat2/build'
+include { SALMON_INDEX                      } from '../../../modules/nf-core/salmon/index'
+include { RSEM_PREPAREREFERENCE as RSEM_PREPAREREFERENCE_GENOME } from '../../../modules/nf-core/rsem/preparereference'
+include { RSEM_PREPAREREFERENCE as MAKE_TRANSCRIPTS_FASTA       } from '../../../modules/nf-core/rsem/preparereference'
 
-include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../modules/local/preprocess_transcripts_fasta_gencode'
-include { GTF2BED                              } from '../../modules/local/gtf2bed'
-include { CAT_ADDITIONAL_FASTA                 } from '../../modules/local/cat_additional_fasta'
-include { GTF_GENE_FILTER                      } from '../../modules/local/gtf_gene_filter'
-include { STAR_GENOMEGENERATE_IGENOMES         } from '../../modules/local/star_genomegenerate_igenomes'
+include { PREPROCESS_TRANSCRIPTS_FASTA_GENCODE } from '../../../modules/local/preprocess_transcripts_fasta_gencode'
+include { GTF2BED                              } from '../../../modules/local/gtf2bed'
+include { CAT_ADDITIONAL_FASTA                 } from '../../../modules/local/cat_additional_fasta'
+include { GTF_GENE_FILTER                      } from '../../../modules/local/gtf_gene_filter'
+include { STAR_GENOMEGENERATE_IGENOMES         } from '../../../modules/local/star_genomegenerate_igenomes'
 
 workflow PREPARE_GENOME {
     take:
diff --git a/subworkflows/local/quantify_rsem.nf b/subworkflows/local/quantify_rsem/main.nf
similarity index 92%
rename from subworkflows/local/quantify_rsem.nf
rename to subworkflows/local/quantify_rsem/main.nf
index 666af33b1..4b7473634 100644
--- a/subworkflows/local/quantify_rsem.nf
+++ b/subworkflows/local/quantify_rsem/main.nf
@@ -2,9 +2,9 @@
 // Gene/transcript quantification with RSEM
 //
 
-include { RSEM_CALCULATEEXPRESSION } from '../../modules/nf-core/rsem/calculateexpression/main'
-include { RSEM_MERGE_COUNTS        } from '../../modules/local/rsem_merge_counts'
-include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main'
+include { RSEM_CALCULATEEXPRESSION } from '../../../modules/nf-core/rsem/calculateexpression'
+include { RSEM_MERGE_COUNTS        } from '../../../modules/local/rsem_merge_counts'
+include { BAM_SORT_STATS_SAMTOOLS  } from '../../nf-core/bam_sort_stats_samtools'
 
 workflow QUANTIFY_RSEM {
     take:
diff --git a/subworkflows/local/quantify_salmon.nf b/subworkflows/local/quantify_salmon/main.nf
similarity index 88%
rename from subworkflows/local/quantify_salmon.nf
rename to subworkflows/local/quantify_salmon/main.nf
index 4ab996b2c..1b936d6fe 100644
--- a/subworkflows/local/quantify_salmon.nf
+++ b/subworkflows/local/quantify_salmon/main.nf
@@ -2,14 +2,14 @@
 // Pseudo-alignment and quantification with Salmon
 //
 
-include { SALMON_QUANT    } from '../../modules/nf-core/salmon/quant/main'
-include { SALMON_TX2GENE  } from '../../modules/local/salmon_tx2gene'
-include { SALMON_TXIMPORT } from '../../modules/local/salmon_tximport'
-
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE               } from '../../modules/local/salmon_summarizedexperiment'
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../modules/local/salmon_summarizedexperiment'
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED        } from '../../modules/local/salmon_summarizedexperiment'
-include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT         } from '../../modules/local/salmon_summarizedexperiment'
+include { SALMON_QUANT    } from '../../../modules/nf-core/salmon/quant'
+include { SALMON_TX2GENE  } from '../../../modules/local/salmon_tx2gene'
+include { SALMON_TXIMPORT } from '../../../modules/local/salmon_tximport'
+
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE               } from '../../../modules/local/salmon_summarizedexperiment'
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_LENGTH_SCALED } from '../../../modules/local/salmon_summarizedexperiment'
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_GENE_SCALED        } from '../../../modules/local/salmon_summarizedexperiment'
+include { SALMON_SUMMARIZEDEXPERIMENT as SALMON_SE_TRANSCRIPT         } from '../../../modules/local/salmon_summarizedexperiment'
 
 workflow QUANTIFY_SALMON {
     take:
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index 72b7619a4..4c281c865 100755
--- a/workflows/rnaseq.nf
+++ b/workflows/rnaseq.nf
@@ -92,14 +92,14 @@ include { DESEQ2_QC as DESEQ2_QC_SALMON      } from '../modules/local/deseq2_qc'
 include { DUPRADAR                           } from '../modules/local/dupradar'
 include { MULTIQC                            } from '../modules/local/multiqc'
 include { MULTIQC_CUSTOM_BIOTYPE             } from '../modules/local/multiqc_custom_biotype'
-include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem.nf'
+include { UMITOOLS_PREPAREFORRSEM as UMITOOLS_PREPAREFORSALMON } from '../modules/local/umitools_prepareforrsem'
 
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
-include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome'
-include { ALIGN_STAR     } from '../subworkflows/local/align_star'
-include { QUANTIFY_RSEM  } from '../subworkflows/local/quantify_rsem'
+include { PREPARE_GENOME                          } from '../subworkflows/local/prepare_genome'
+include { ALIGN_STAR                              } from '../subworkflows/local/align_star'
+include { QUANTIFY_RSEM                           } from '../subworkflows/local/quantify_rsem'
 include { QUANTIFY_SALMON as QUANTIFY_STAR_SALMON } from '../subworkflows/local/quantify_salmon'
 include { QUANTIFY_SALMON as QUANTIFY_SALMON      } from '../subworkflows/local/quantify_salmon'