diff --git a/conf/modules.config b/conf/modules.config
index 104a515..954e266 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -619,6 +619,16 @@ process {
         memory = { 36.GB * task.attempt }
     }
 
+    withName: ".*:FIMO:SELECT_SIGNIFICANT" {
+        ext.args = {"'NR==1 || \$9 <= ${params.fimo_qvalue_threshold}'"}
+        ext.prefix = {"${meta.id}_significant"}
+        publishDir = [
+            path: { "${params.outdir}/06_fimo/05_significant_results" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     /*
     SNEEP
     */
diff --git a/nextflow.config b/nextflow.config
index 39d80aa..503283e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -40,6 +40,9 @@ params {
     // SNEEP options
     skip_sneep                 = false
 
+    // FIMO options
+    fimo_qvalue_threshold      = 0.05
+
     dynamite_ofolds            = 3
     dynamite_ifolds            = 6
     dynamite_alpha             = 0.1
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6ac9a4b..c43b476 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -270,6 +270,21 @@
                 }
             }
         },
+        "fimo_options": {
+            "title": "FIMO options",
+            "type": "object",
+            "fa_icon": "fas fa-search",
+            "description": "Options for FIMO (Find Individual Motif Occurrences) analysis.",
+            "properties": {
+                "fimo_qvalue_threshold": {
+                    "type": "number",
+                    "default": 0.05,
+                    "description": "Q-value threshold for filtering significant FIMO results.",
+                    "fa_icon": "fas fa-filter",
+                    "help_text": "Q-value threshold for filtering significant FIMO results. Only motif occurrences with q-values below this threshold will be kept. The default value is 0.05."
+                }
+            }
+        },
         "dynamite_options": {
             "title": "DYNAMITE options",
             "type": "object",
@@ -582,6 +597,9 @@
         {
             "$ref": "#/$defs/optional_steps"
         },
+        {
+            "$ref": "#/$defs/fimo_options"
+        },
         {
             "$ref": "#/$defs/dynamite_options"
         },
diff --git a/subworkflows/local/fimo/main.nf b/subworkflows/local/fimo/main.nf
index 9d23437..9e922c1 100644
--- a/subworkflows/local/fimo/main.nf
+++ b/subworkflows/local/fimo/main.nf
@@ -5,6 +5,7 @@ include { GAWK as CONCAT_FILTER_GFF             } from "../../../modules/nf-core
 include { GNU_SORT as SORT_GFF                  } from "../../../modules/nf-core/gnu/sort"
 include { GAWK as CONCAT_FILTER_TSV             } from "../../../modules/nf-core/gawk"
 include { CSVTK_SORT as SORT_TSV                } from '../../../modules/nf-core/csvtk/sort'
+include { GAWK as SELECT_SIGNIFICANT            } from "../../../modules/nf-core/gawk"
 
 workflow FIMO {
     take:
@@ -67,8 +68,12 @@ workflow FIMO {
     SORT_TSV(CONCAT_FILTER_TSV.out.output, 'tsv', 'tsv')
     ch_versions = ch_versions.mix(SORT_TSV.out.versions)
 
+    SELECT_SIGNIFICANT(SORT_TSV.out.sorted, [], false)
+    ch_versions = ch_versions.mix(SELECT_SIGNIFICANT.out.versions)
+
     emit:
-    gff      = SORT_GFF.out.sorted
-    tsv      = SORT_TSV.out.sorted
-    versions = ch_versions
+    gff             = SORT_GFF.out.sorted
+    tsv             = SORT_TSV.out.sorted
+    tsv_significant = SELECT_SIGNIFICANT.out.output
+    versions        = ch_versions
 }
diff --git a/subworkflows/local/fimo/tests/main.nf.test.snap b/subworkflows/local/fimo/tests/main.nf.test.snap
index baa1ff7..74109e5 100644
--- a/subworkflows/local/fimo/tests/main.nf.test.snap
+++ b/subworkflows/local/fimo/tests/main.nf.test.snap
@@ -19,6 +19,14 @@
                     ]
                 ],
                 "2": [
+                    [
+                        {
+                            "id": "L10_chromHMM_promoters"
+                        },
+                        "L10_chromHMM_promoters_significant.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
                     "versions.yml:md5,09deaa382cdc983ffad29500b0c47210",
                     "versions.yml:md5,270cc8fd3cf5da52f09e2bcfb66844d1",
                     "versions.yml:md5,37d1f45c834fbc3c356023cdfed0918a",
@@ -26,6 +34,7 @@
                     "versions.yml:md5,612da238fbeb03191d349ddc72093946",
                     "versions.yml:md5,612da238fbeb03191d349ddc72093946",
                     "versions.yml:md5,c1dfd15a1f2163efd0fc318809c8a071",
+                    "versions.yml:md5,d9cf2bc9a6b5f0916586f0b5184b580f",
                     "versions.yml:md5,def0f65b2a7925e2541586ea7ad06118",
                     "versions.yml:md5,e50e1883b0220a195e1c520411dcbc63"
                 ],
@@ -45,6 +54,14 @@
                         "L10_chromHMM_promoters.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "tsv_significant": [
+                    [
+                        {
+                            "id": "L10_chromHMM_promoters"
+                        },
+                        "L10_chromHMM_promoters_significant.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,09deaa382cdc983ffad29500b0c47210",
                     "versions.yml:md5,270cc8fd3cf5da52f09e2bcfb66844d1",
@@ -53,6 +70,7 @@
                     "versions.yml:md5,612da238fbeb03191d349ddc72093946",
                     "versions.yml:md5,612da238fbeb03191d349ddc72093946",
                     "versions.yml:md5,c1dfd15a1f2163efd0fc318809c8a071",
+                    "versions.yml:md5,d9cf2bc9a6b5f0916586f0b5184b580f",
                     "versions.yml:md5,def0f65b2a7925e2541586ea7ad06118",
                     "versions.yml:md5,e50e1883b0220a195e1c520411dcbc63"
                 ]
@@ -60,9 +78,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-28T13:45:59.335325874"
+        "timestamp": "2025-11-13T18:36:04.422878191"
     },
     "Should run without failures": {
         "content": [
@@ -80,16 +98,25 @@
                         {
                             "id": "L10_chromHMM_promoters"
                         },
-                        "L10_chromHMM_promoters.tsv:md5,b9dccc98df70fa127fed3ec9f5d2b0cd"
+                        "L10_chromHMM_promoters.tsv:md5,903892dbd88b1cf1fe69f6e85ede5974"
                     ]
                 ],
                 "2": [
+                    [
+                        {
+                            "id": "L10_chromHMM_promoters"
+                        },
+                        "L10_chromHMM_promoters_significant.tsv:md5,6ec71314deae3fb80be236a018899406"
+                    ]
+                ],
+                "3": [
                     "versions.yml:md5,270cc8fd3cf5da52f09e2bcfb66844d1",
                     "versions.yml:md5,37d1f45c834fbc3c356023cdfed0918a",
                     "versions.yml:md5,612da238fbeb03191d349ddc72093946",
                     "versions.yml:md5,612da238fbeb03191d349ddc72093946",
                     "versions.yml:md5,91d4e73ea846dae7e805279e47204dc7",
                     "versions.yml:md5,c1dfd15a1f2163efd0fc318809c8a071",
+                    "versions.yml:md5,d9cf2bc9a6b5f0916586f0b5184b580f",
                     "versions.yml:md5,def0f65b2a7925e2541586ea7ad06118",
                     "versions.yml:md5,e50e1883b0220a195e1c520411dcbc63"
                 ],
@@ -106,7 +133,15 @@
                         {
                             "id": "L10_chromHMM_promoters"
                         },
-                        "L10_chromHMM_promoters.tsv:md5,b9dccc98df70fa127fed3ec9f5d2b0cd"
+                        "L10_chromHMM_promoters.tsv:md5,903892dbd88b1cf1fe69f6e85ede5974"
+                    ]
+                ],
+                "tsv_significant": [
+                    [
+                        {
+                            "id": "L10_chromHMM_promoters"
+                        },
+                        "L10_chromHMM_promoters_significant.tsv:md5,6ec71314deae3fb80be236a018899406"
                     ]
                 ],
                 "versions": [
@@ -116,6 +151,7 @@
                     "versions.yml:md5,612da238fbeb03191d349ddc72093946",
                     "versions.yml:md5,91d4e73ea846dae7e805279e47204dc7",
                     "versions.yml:md5,c1dfd15a1f2163efd0fc318809c8a071",
+                    "versions.yml:md5,d9cf2bc9a6b5f0916586f0b5184b580f",
                     "versions.yml:md5,def0f65b2a7925e2541586ea7ad06118",
                     "versions.yml:md5,e50e1883b0220a195e1c520411dcbc63"
                 ]
@@ -123,8 +159,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-28T13:45:35.150219947"
+        "timestamp": "2025-11-13T18:35:49.650684716"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/fimo/tests/nextflow.config b/subworkflows/local/fimo/tests/nextflow.config
index d4f8b01..88a79a4 100644
--- a/subworkflows/local/fimo/tests/nextflow.config
+++ b/subworkflows/local/fimo/tests/nextflow.config
@@ -12,7 +12,12 @@ process {
         ext.args = "-v HEADER='motif_id\\tmotif_alt_id\\tsequence_name\\tstart\\tstop\\tstrand\\tscore\\tp-value\\tq-value\\tmatched_sequence' 'BEGIN {print HEADER} FNR==1 {next} /^#/ {next} NF==0 {next} {print}'"
     }
 
-    withName: ".*:FIMO:SORT_TSV" {
+    withName: "FIMO:SORT_TSV" {
         ext.args = "-k motif_id:N -k sequence_name:N -k start:n -k stop:n -k strand -k score:nr -k p-value:n -k q-value:n -k matched_sequence"
     }
+
+    withName: "FIMO:SELECT_SIGNIFICANT" {
+        ext.args = {"'NR==1 || \$9 <= 0.4'"}
+        ext.prefix = {"${meta.id}_significant"}
+    }
 }
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 0a0aafa..d52d72a 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -1,7 +1,7 @@
 {
     "Should run with bed only": {
         "content": [
-            174,
+            179,
             {
                 "AFFINITY_MEAN": {
                     "numpy": "2.2.6",
@@ -143,6 +143,9 @@
                 "RUN_FIMO": {
                     "fimo": "5.5.8"
                 },
+                "SELECT_SIGNIFICANT": {
+                    "gawk": "5.3.0"
+                },
                 "SORT_BED": {
                     "coreutils": 9.3
                 },
@@ -599,6 +602,12 @@
                 "06_fimo/04_combined_results/tsv/L1_H3K4me3.tsv",
                 "06_fimo/04_combined_results/tsv/p6_H3K27ac.tsv",
                 "06_fimo/04_combined_results/tsv/p6_H3K4me3.tsv",
+                "06_fimo/05_significant_results",
+                "06_fimo/05_significant_results/L10_H3K27ac_significant.tsv",
+                "06_fimo/05_significant_results/L1_H3K27ac_significant.tsv",
+                "06_fimo/05_significant_results/L1_H3K4me3_significant.tsv",
+                "06_fimo/05_significant_results/p6_H3K27ac_significant.tsv",
+                "06_fimo/05_significant_results/p6_H3K4me3_significant.tsv",
                 "07_sneep",
                 "07_sneep/01_filtered_scales_motifs",
                 "07_sneep/01_filtered_scales_motifs/filtered_sneep_scale_mouse_218.txt",
@@ -3949,6 +3958,11 @@
                 "L1_H3K4me3.tsv:md5,234fdab4f7c07b423f8f022b6c3d0d8a",
                 "p6_H3K27ac.tsv:md5,d75f51f8af229ad6082a3bbe38f94f14",
                 "p6_H3K4me3.tsv:md5,b1004c2222c3b0e75062dbb0083d46eb",
+                "L10_H3K27ac_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "L1_H3K27ac_significant.tsv:md5,0700a8ce866a2ca40795461eecf1bdf6",
+                "L1_H3K4me3_significant.tsv:md5,a2b971328c33a981678d90d16849c272",
+                "p6_H3K27ac_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "p6_H3K4me3_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
                 "filtered_sneep_scale_mouse_218.txt:md5,26199aaf8103de723163c03bfa8b88b2",
                 "filtered_sneep_transfac_mouse_218.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "L10_H3K27ac.bed:md5,4e48a06e991fdd12712c25823eebc5be",
@@ -3975,13 +3989,13 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-28T13:58:48.753999494"
+        "timestamp": "2025-11-13T19:36:12.666238946"
     },
     "Should run with both bed and bam input": {
         "content": [
-            396,
+            407,
             {
                 "AFFINITY_MEAN": {
                     "numpy": "2.2.6",
@@ -4148,6 +4162,9 @@
                 "RUN_FIMO": {
                     "fimo": "5.5.8"
                 },
+                "SELECT_SIGNIFICANT": {
+                    "gawk": "5.3.0"
+                },
                 "SORT_BED": {
                     "coreutils": 9.3
                 },
@@ -5163,6 +5180,18 @@
                 "06_fimo/04_combined_results/tsv/p6_H3K4me3.tsv",
                 "06_fimo/04_combined_results/tsv/p6_chromHMM_enhancers.tsv",
                 "06_fimo/04_combined_results/tsv/p6_chromHMM_promoters.tsv",
+                "06_fimo/05_significant_results",
+                "06_fimo/05_significant_results/L10_H3K27ac_significant.tsv",
+                "06_fimo/05_significant_results/L10_chromHMM_enhancers_significant.tsv",
+                "06_fimo/05_significant_results/L10_chromHMM_promoters_significant.tsv",
+                "06_fimo/05_significant_results/L1_H3K27ac_significant.tsv",
+                "06_fimo/05_significant_results/L1_H3K4me3_significant.tsv",
+                "06_fimo/05_significant_results/L1_chromHMM_enhancers_significant.tsv",
+                "06_fimo/05_significant_results/L1_chromHMM_promoters_significant.tsv",
+                "06_fimo/05_significant_results/p6_H3K27ac_significant.tsv",
+                "06_fimo/05_significant_results/p6_H3K4me3_significant.tsv",
+                "06_fimo/05_significant_results/p6_chromHMM_enhancers_significant.tsv",
+                "06_fimo/05_significant_results/p6_chromHMM_promoters_significant.tsv",
                 "07_sneep",
                 "07_sneep/01_filtered_scales_motifs",
                 "07_sneep/01_filtered_scales_motifs/filtered_sneep_scale_mouse_218.txt",
@@ -10054,6 +10083,17 @@
                 "p6_H3K4me3.tsv:md5,264817038ac5cd1062b224364c96a451",
                 "p6_chromHMM_enhancers.tsv:md5,38f7bdbc36fbe617905a88934d402630",
                 "p6_chromHMM_promoters.tsv:md5,95a3cfa56a471160f6d1d2b35ddd5362",
+                "L10_H3K27ac_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "L10_chromHMM_enhancers_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "L10_chromHMM_promoters_significant.tsv:md5,8a21488440735b59233f13af69d9d387",
+                "L1_H3K27ac_significant.tsv:md5,0700a8ce866a2ca40795461eecf1bdf6",
+                "L1_H3K4me3_significant.tsv:md5,a2b971328c33a981678d90d16849c272",
+                "L1_chromHMM_enhancers_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "L1_chromHMM_promoters_significant.tsv:md5,4695ea8aec0374345d4276338add6d75",
+                "p6_H3K27ac_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "p6_H3K4me3_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "p6_chromHMM_enhancers_significant.tsv:md5,cd7825b546b90fc8e7a8eb1cc8533ca3",
+                "p6_chromHMM_promoters_significant.tsv:md5,188507b513f0016ecb82965de3b58bd7",
                 "filtered_sneep_scale_mouse_218.txt:md5,26199aaf8103de723163c03bfa8b88b2",
                 "filtered_sneep_transfac_mouse_218.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "L10_H3K27ac.bed:md5,59f68dd95564876b3fe43e9af1195bfa",
@@ -10104,8 +10144,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-28T13:53:09.941876368"
+        "timestamp": "2025-11-13T19:32:43.987079271"
     }
 }
\ No newline at end of file
diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf
index 2220dde..41088c2 100644
--- a/workflows/tfactivity.nf
+++ b/workflows/tfactivity.nf
@@ -147,7 +147,7 @@ workflow TFACTIVITY {
             MOTIFS.out.meme,
         )
         ch_versions = ch_versions.mix(FIMO.out.versions)
-        ch_fimo_binding_sites = FIMO.out.tsv
+        ch_fimo_binding_sites = FIMO.out.tsv_significant
     }
 
     if (!params.skip_sneep) {