diff --git a/modules/nf-core/bismark/align/nextflow.config b/conf/modules/bismark_align.config
similarity index 99%
rename from modules/nf-core/bismark/align/nextflow.config
rename to conf/modules/bismark_align.config
index 7e6e83b6..57c74ec9 100644
--- a/modules/nf-core/bismark/align/nextflow.config
+++ b/conf/modules/bismark_align.config
@@ -35,4 +35,4 @@ process {
                 ]
             ]
         }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bismark/coverage2cytosine/nextflow.config b/conf/modules/bismark_coverage2cytosine.config
similarity index 99%
rename from modules/nf-core/bismark/coverage2cytosine/nextflow.config
rename to conf/modules/bismark_coverage2cytosine.config
index f1a83fb7..8737c561 100644
--- a/modules/nf-core/bismark/coverage2cytosine/nextflow.config
+++ b/conf/modules/bismark_coverage2cytosine.config
@@ -19,4 +19,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bismark/deduplicate/nextflow.config b/conf/modules/bismark_deduplicate.config
similarity index 99%
rename from modules/nf-core/bismark/deduplicate/nextflow.config
rename to conf/modules/bismark_deduplicate.config
index b2b51c29..be770f44 100644
--- a/modules/nf-core/bismark/deduplicate/nextflow.config
+++ b/conf/modules/bismark_deduplicate.config
@@ -9,4 +9,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bismark/genomepreparation/nextflow.config b/conf/modules/bismark_genomepreparation.config
similarity index 99%
rename from modules/nf-core/bismark/genomepreparation/nextflow.config
rename to conf/modules/bismark_genomepreparation.config
index ed506125..94c3592f 100644
--- a/modules/nf-core/bismark/genomepreparation/nextflow.config
+++ b/conf/modules/bismark_genomepreparation.config
@@ -11,4 +11,4 @@ process {
             enabled: params.save_reference
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bismark/methylationextractor/nextflow.config b/conf/modules/bismark_methylationextractor.config
similarity index 99%
rename from modules/nf-core/bismark/methylationextractor/nextflow.config
rename to conf/modules/bismark_methylationextractor.config
index b312885b..a1f69088 100644
--- a/modules/nf-core/bismark/methylationextractor/nextflow.config
+++ b/conf/modules/bismark_methylationextractor.config
@@ -38,4 +38,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bismark/report/nextflow.config b/conf/modules/bismark_report.config
similarity index 99%
rename from modules/nf-core/bismark/report/nextflow.config
rename to conf/modules/bismark_report.config
index 597a4684..27e98821 100644
--- a/modules/nf-core/bismark/report/nextflow.config
+++ b/conf/modules/bismark_report.config
@@ -7,4 +7,4 @@ process {
             pattern: "*.html"
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bismark/summary/nextflow.config b/conf/modules/bismark_summary.config
similarity index 99%
rename from modules/nf-core/bismark/summary/nextflow.config
rename to conf/modules/bismark_summary.config
index ded23dda..92a5d4c0 100644
--- a/modules/nf-core/bismark/summary/nextflow.config
+++ b/conf/modules/bismark_summary.config
@@ -7,4 +7,4 @@ process {
             pattern: "*.{html,txt}"
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bwameth/align/nextflow.config b/conf/modules/bwameth_align.config
similarity index 99%
rename from modules/nf-core/bwameth/align/nextflow.config
rename to conf/modules/bwameth_align.config
index d5cbe70d..d660b174 100644
--- a/modules/nf-core/bwameth/align/nextflow.config
+++ b/conf/modules/bwameth_align.config
@@ -8,4 +8,4 @@ process {
                 enabled: params.save_align_intermeds
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bwameth/index/nextflow.config b/conf/modules/bwameth_index.config
similarity index 99%
rename from modules/nf-core/bwameth/index/nextflow.config
rename to conf/modules/bwameth_index.config
index 92d4e632..74559b06 100644
--- a/modules/nf-core/bwameth/index/nextflow.config
+++ b/conf/modules/bwameth_index.config
@@ -8,4 +8,4 @@ process {
             enabled: params.save_reference
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/fastqc/nextflow.config b/conf/modules/fastqc.config
similarity index 99%
rename from modules/nf-core/fastqc/nextflow.config
rename to conf/modules/fastqc.config
index 7e31c74d..f611d032 100644
--- a/modules/nf-core/fastqc/nextflow.config
+++ b/conf/modules/fastqc.config
@@ -14,4 +14,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/methyldackel/extract/nextflow.config b/conf/modules/methyldackel_extract.config
similarity index 99%
rename from modules/nf-core/methyldackel/extract/nextflow.config
rename to conf/modules/methyldackel_extract.config
index f7e24c73..ca274f3d 100644
--- a/modules/nf-core/methyldackel/extract/nextflow.config
+++ b/conf/modules/methyldackel_extract.config
@@ -19,4 +19,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/methyldackel/mbias/nextflow.config b/conf/modules/methyldackel_mbias.config
similarity index 99%
rename from modules/nf-core/methyldackel/mbias/nextflow.config
rename to conf/modules/methyldackel_mbias.config
index 8ae58f00..3fc655d3 100644
--- a/modules/nf-core/methyldackel/mbias/nextflow.config
+++ b/conf/modules/methyldackel_mbias.config
@@ -12,4 +12,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/multiqc/nextflow.config b/conf/modules/multiqc.config
similarity index 99%
rename from modules/nf-core/multiqc/nextflow.config
rename to conf/modules/multiqc.config
index 98cf050f..3334a8ec 100644
--- a/modules/nf-core/multiqc/nextflow.config
+++ b/conf/modules/multiqc.config
@@ -7,4 +7,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/picard/markduplicates/nextflow.config b/conf/modules/picard_markduplicates.config
similarity index 99%
rename from modules/nf-core/picard/markduplicates/nextflow.config
rename to conf/modules/picard_markduplicates.config
index 1c3c2ec7..ea2368dc 100644
--- a/modules/nf-core/picard/markduplicates/nextflow.config
+++ b/conf/modules/picard_markduplicates.config
@@ -15,4 +15,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/preseq/lcextrap/nextflow.config b/conf/modules/preseq_lcextrap.config
similarity index 99%
rename from modules/nf-core/preseq/lcextrap/nextflow.config
rename to conf/modules/preseq_lcextrap.config
index 827ef5ed..09e4768e 100644
--- a/modules/nf-core/preseq/lcextrap/nextflow.config
+++ b/conf/modules/preseq_lcextrap.config
@@ -14,4 +14,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/qualimap/bamqc/nextflow.config b/conf/modules/qualimap_bamqc.config
similarity index 99%
rename from modules/nf-core/qualimap/bamqc/nextflow.config
rename to conf/modules/qualimap_bamqc.config
index 004b4047..ad9688ba 100644
--- a/modules/nf-core/qualimap/bamqc/nextflow.config
+++ b/conf/modules/qualimap_bamqc.config
@@ -5,4 +5,4 @@ process {
             params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : ''
         ].join(" ").trim()
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/samtools/faidx/nextflow.config b/conf/modules/samtools_faidx.config
similarity index 99%
rename from modules/nf-core/samtools/faidx/nextflow.config
rename to conf/modules/samtools_faidx.config
index 8b2368a6..26bb23f9 100644
--- a/modules/nf-core/samtools/faidx/nextflow.config
+++ b/conf/modules/samtools_faidx.config
@@ -8,4 +8,4 @@ process {
             pattern: "*.fai"
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/samtools/flagstat/nextflow.config b/conf/modules/samtools_flagstat.config
similarity index 99%
rename from modules/nf-core/samtools/flagstat/nextflow.config
rename to conf/modules/samtools_flagstat.config
index 2cf4ca87..4b79875c 100644
--- a/modules/nf-core/samtools/flagstat/nextflow.config
+++ b/conf/modules/samtools_flagstat.config
@@ -8,4 +8,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/samtools/index/nextflow.config b/conf/modules/samtools_index.config
similarity index 99%
rename from modules/nf-core/samtools/index/nextflow.config
rename to conf/modules/samtools_index.config
index 5131f953..76cf0fd7 100644
--- a/modules/nf-core/samtools/index/nextflow.config
+++ b/conf/modules/samtools_index.config
@@ -16,4 +16,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/samtools/sort/nextflow.config b/conf/modules/samtools_sort.config
similarity index 99%
rename from modules/nf-core/samtools/sort/nextflow.config
rename to conf/modules/samtools_sort.config
index bfb6eb1e..95c78bd0 100644
--- a/modules/nf-core/samtools/sort/nextflow.config
+++ b/conf/modules/samtools_sort.config
@@ -27,4 +27,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/samtools/stats/nextflow.config b/conf/modules/samtools_stats.config
similarity index 99%
rename from modules/nf-core/samtools/stats/nextflow.config
rename to conf/modules/samtools_stats.config
index 285e24d7..7574f62f 100644
--- a/modules/nf-core/samtools/stats/nextflow.config
+++ b/conf/modules/samtools_stats.config
@@ -8,4 +8,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/trimgalore/nextflow.config b/conf/modules/trimgalore.config
similarity index 99%
rename from modules/nf-core/trimgalore/nextflow.config
rename to conf/modules/trimgalore.config
index 6c33f5c4..95b6b1cf 100644
--- a/modules/nf-core/trimgalore/nextflow.config
+++ b/conf/modules/trimgalore.config
@@ -87,4 +87,4 @@ process {
             ]
         ]
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/local/bwameth/nextflow.config b/subworkflows/local/bwameth/nextflow.config
index 4eff78d7..19f4011e 100644
--- a/subworkflows/local/bwameth/nextflow.config
+++ b/subworkflows/local/bwameth/nextflow.config
@@ -1,12 +1,11 @@
 
-includeConfig "../../../modules/nf-core/bwameth/align/nextflow.config"
-includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config"
-
-includeConfig "../../../modules/nf-core/samtools/flagstat/nextflow.config"
-includeConfig "../../../modules/nf-core/samtools/stats/nextflow.config"
-includeConfig "../../../modules/nf-core/picard/markduplicates/nextflow.config"
-includeConfig "../../../modules/nf-core/methyldackel/extract/nextflow.config"
-includeConfig "../../../modules/nf-core/methyldackel/mbias/nextflow.config"
+includeConfig "../../../conf/modules/bwameth_align.config"
+includeConfig "../../../conf/modules/samtools_sort.config"
+includeConfig "../../../conf/modules/samtools_flagstat.config"
+includeConfig "../../../conf/modules/samtools_stats.config"
+includeConfig "../../../conf/modules/picard_markduplicates.config"
+includeConfig "../../../conf/modules/methyldackel_extract.config"
+includeConfig "../../../conf/modules/methyldackel_mbias.config"
 
 process {
 
diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config b/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config
index 39f3f167..c4bb551b 100644
--- a/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config
+++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config
@@ -1,4 +1,4 @@
 
-includeConfig "../../../modules/nf-core/bismark/genomepreparation/nextflow.config"
-includeConfig "../../../modules/nf-core/samtools/faidx/nextflow.config"
-includeConfig "../../../modules/nf-core/bwameth/index/nextflow.config"
+includeConfig "../../../conf/modules/bismark_genomepreparation.config"
+includeConfig "../../../conf/modules/samtools_faidx.config"
+includeConfig "../../../conf/modules/bwameth_index.config"
diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config
index 03e07673..c8e3aa92 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config
+++ b/subworkflows/nf-core/fastq_align_dedup_bismark/nextflow.config
@@ -1,8 +1,8 @@
-includeConfig "../../../modules/nf-core/bismark/align/nextflow.config"
-includeConfig "../../../modules/nf-core/bismark/deduplicate/nextflow.config"
-includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config"
-includeConfig "../../../modules/nf-core/samtools/index/nextflow.config"
-includeConfig "../../../modules/nf-core/bismark/methylationextractor/nextflow.config"
-includeConfig "../../../modules/nf-core/bismark/coverage2cytosine/nextflow.config"
-includeConfig "../../../modules/nf-core/bismark/report/nextflow.config"
-includeConfig "../../../modules/nf-core/bismark/summary/nextflow.config"
\ No newline at end of file
+includeConfig "../../../conf/modules/bismark_align.config"
+includeConfig "../../../conf/modules/bismark_deduplicate.config"
+includeConfig "../../../conf/modules/samtools_sort.config"
+includeConfig "../../../conf/modules/samtools_index.config"
+includeConfig "../../../conf/modules/bismark_methylationextractor.config"
+includeConfig "../../../conf/modules/bismark_coverage2cytosine.config"
+includeConfig "../../../conf/modules/bismark_report.config"
+includeConfig "../../../conf/modules/bismark_summary.config"
\ No newline at end of file
diff --git a/workflows/methylseq/nextflow.config b/workflows/methylseq/nextflow.config
index 506311f2..202d7b9c 100644
--- a/workflows/methylseq/nextflow.config
+++ b/workflows/methylseq/nextflow.config
@@ -1,9 +1,9 @@
 // module configs
-includeConfig "../../modules/nf-core/fastqc/nextflow.config"
-includeConfig "../../modules/nf-core/trimgalore/nextflow.config"
-includeConfig "../../modules/nf-core/multiqc/nextflow.config"
-includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config"
-includeConfig "../../modules/nf-core/qualimap/bamqc/nextflow.config"
+includeConfig "../../conf/modules/fastqc.config"
+includeConfig "../../conf/modules/trimgalore.config"
+includeConfig "../../conf/modules/multiqc.config"
+includeConfig "../../conf/modules/preseq_lcextrap.config"
+includeConfig "../../conf/modules/qualimap_bamqc.config"
 
 // subworkflow configs
 includeConfig "../../subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config"