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Merged
LeonHafner merged 5 commits into from
Nov 19, 2025
Merged

Add significance filter for FIMO results #65

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00fa699
Replace 'Channel' with 'channel' as prior is deprecated
nictru Nov 11, 2025
a3bdcf1
Add significant binding sites filter
nictru Nov 12, 2025
f3efe26
Revert "Replace 'Channel' with 'channel' as prior is deprecated"
nictru Nov 12, 2025
a1628a1
Fix failing FIMO tests
nictru Nov 13, 2025
78a4054
Update pipeline-level test snapshots
nictru Nov 13, 2025
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10 changes: 10 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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
*/
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3 changes: 3 additions & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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18 changes: 18 additions & 0 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -582,6 +597,9 @@
{
"$ref": "#/$defs/optional_steps"
},
{
"$ref": "#/$defs/fimo_options"
},
{
"$ref": "#/$defs/dynamite_options"
},
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11 changes: 8 additions & 3 deletions subworkflows/local/fimo/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down Expand Up @@ -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
}
48 changes: 42 additions & 6 deletions subworkflows/local/fimo/tests/main.nf.test.snap
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Expand Up @@ -19,13 +19,22 @@
]
],
"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",
"versions.yml:md5,612da238fbeb03191d349ddc72093946",
"versions.yml:md5,612da238fbeb03191d349ddc72093946",
"versions.yml:md5,612da238fbeb03191d349ddc72093946",
"versions.yml:md5,c1dfd15a1f2163efd0fc318809c8a071",
"versions.yml:md5,d9cf2bc9a6b5f0916586f0b5184b580f",
"versions.yml:md5,def0f65b2a7925e2541586ea7ad06118",
"versions.yml:md5,e50e1883b0220a195e1c520411dcbc63"
],
Expand All @@ -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",
Expand All @@ -53,16 +70,17 @@
"versions.yml:md5,612da238fbeb03191d349ddc72093946",
"versions.yml:md5,612da238fbeb03191d349ddc72093946",
"versions.yml:md5,c1dfd15a1f2163efd0fc318809c8a071",
"versions.yml:md5,d9cf2bc9a6b5f0916586f0b5184b580f",
"versions.yml:md5,def0f65b2a7925e2541586ea7ad06118",
"versions.yml:md5,e50e1883b0220a195e1c520411dcbc63"
]
}
],
"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": [
Expand All @@ -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"
],
Expand All @@ -106,7 +133,15 @@
{
"id": "L10_chromHMM_promoters"
},
"L10_chromHMM_promoters.tsv:md5,b9dccc98df70fa127fed3ec9f5d2b0cd"
Comment thread
LeonHafner marked this conversation as resolved.
"L10_chromHMM_promoters.tsv:md5,903892dbd88b1cf1fe69f6e85ede5974"
]
],
"tsv_significant": [
[
{
"id": "L10_chromHMM_promoters"
},
"L10_chromHMM_promoters_significant.tsv:md5,6ec71314deae3fb80be236a018899406"
]
],
"versions": [
Expand All @@ -116,15 +151,16 @@
"versions.yml:md5,612da238fbeb03191d349ddc72093946",
"versions.yml:md5,91d4e73ea846dae7e805279e47204dc7",
"versions.yml:md5,c1dfd15a1f2163efd0fc318809c8a071",
"versions.yml:md5,d9cf2bc9a6b5f0916586f0b5184b580f",
"versions.yml:md5,def0f65b2a7925e2541586ea7ad06118",
"versions.yml:md5,e50e1883b0220a195e1c520411dcbc63"
]
}
],
"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"
}
}
7 changes: 6 additions & 1 deletion subworkflows/local/fimo/tests/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Comment thread
LeonHafner marked this conversation as resolved.
}

withName: "FIMO:SELECT_SIGNIFICANT" {
ext.args = {"'NR==1 || \$9 <= 0.4'"}
ext.prefix = {"${meta.id}_significant"}
}
}
52 changes: 46 additions & 6 deletions tests/default.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"Should run with bed only": {
"content": [
174,
179,
{
"AFFINITY_MEAN": {
"numpy": "2.2.6",
Expand Down Expand Up @@ -143,6 +143,9 @@
"RUN_FIMO": {
"fimo": "5.5.8"
},
"SELECT_SIGNIFICANT": {
"gawk": "5.3.0"
},
"SORT_BED": {
"coreutils": 9.3
},
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand All @@ -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",
Expand Down Expand Up @@ -4148,6 +4162,9 @@
"RUN_FIMO": {
"fimo": "5.5.8"
},
"SELECT_SIGNIFICANT": {
"gawk": "5.3.0"
},
"SORT_BED": {
"coreutils": 9.3
},
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
}
2 changes: 1 addition & 1 deletion workflows/tfactivity.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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) {
Expand Down