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Merged
DLBPointon merged 2 commits into from
Sep 1, 2026
Merged

Update to add flag for dot replacement #12843

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8540e97
Update to add flag for dot replacement
DLBPointon Aug 28, 2026
566a7e9
Merge branch 'master' into fcf_update_1
DLBPointon Aug 28, 2026
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25 changes: 17 additions & 8 deletions subworkflows/nf-core/fasta_clean_faidx/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ include { SAMTOOLS_DICT } from "../../../modules/nf-core/samtool
workflow FASTA_CLEAN_FAIDX {
take:
ch_reference // channel.of( [meta], reference )
val_replace_dots // boolean: replace dots in headers with underscores in trimmed reference
val_get_chromsizes // boolean: emit chromsizes
val_get_dict // boolean: emit dict

Expand Down Expand Up @@ -50,19 +51,27 @@ workflow FASTA_CLEAN_FAIDX {
//
// MODULE: REPLACE `.` IN HEADERS WITH `_`
// `.` CAN CAUSE ISSUES FOR SOME DOWNSTREAM TOOLS
//
SEQKIT_DOTS (
SEQKIT_SEQ.out.fastx,
"fasta"
)
// CONTROLLING THIS ON val_replace_dots ALLOWS US TO STAY INSIDE OF
// SOME STANDARDS (e.g. ONLY TAKE FIRST WORK IN HEADER)
//
if (val_replace_dots) {
SEQKIT_DOTS (
SEQKIT_SEQ.out.fastx,
"fasta"
)

renamed_fasta = SEQKIT_DOTS.out.fastx
} else {
renamed_fasta = SEQKIT_SEQ.out.fastx
}


//
// MODULE: GENERATE INDEX OF REFERENCE FASTA
// OPTIONALLY EMIT CHROMOSOME SIZES FILE
//
SAMTOOLS_FAIDX (
SEQKIT_DOTS.out.fastx.map { meta, file -> [meta, file, []] },
renamed_fasta.map { meta, file -> [meta, file, []] },
val_get_chromsizes
)

Expand All @@ -79,12 +88,12 @@ workflow FASTA_CLEAN_FAIDX {
// MODULE: GENERATE A SAMTOOLS DICT FILE BASED ON THE CORRECTED FASTA FILE
//
SAMTOOLS_DICT (
SEQKIT_DOTS.out.fastx.filter { meta, file -> val_get_dict }
renamed_fasta.filter { meta, file -> val_get_dict }
)


emit:
reference = SEQKIT_DOTS.out.fastx
reference = renamed_fasta
fai = SAMTOOLS_FAIDX.out.fai
sizes = SAMTOOLS_FAIDX.out.sizes
dict = SAMTOOLS_DICT.out.dict
Expand Down
10 changes: 10 additions & 0 deletions subworkflows/nf-core/fasta_clean_faidx/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,20 @@ input:

Structure: [ val(meta), path(fasta) ]
pattern: "*.{(fasta,fa,fna)(.gz)}"

- val_replace_dots:
type: boolean
description: |
Whether to replace dots in the fasta reference name with underscores.

Some tools can't handle dots in the fasta name, however,
sometimes the ID must remain unchanged.

- val_get_chromsizes:
type: boolean
description: |
Whether to generate a chromosome sizes file from the fasta reference.

- val_get_dict:
type: boolean
description: |
Expand Down
48 changes: 46 additions & 2 deletions subworkflows/nf-core/fasta_clean_faidx/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ nextflow_workflow {
)
input[1] = true
input[2] = true
input[3] = true
"""
}

Expand All @@ -41,6 +42,7 @@ nextflow_workflow {
{ assert workflow.success },
{ assert snapshot(
path(workflow.out.dict[0][1]).readLines()[0],
path(workflow.out.reference[0][1]).readLines()[0],
workflow.out.reference,
workflow.out.fai,
workflow.out.sizes,
Expand All @@ -50,7 +52,7 @@ nextflow_workflow {
}
}

test("Bacteroides fragilis genome [fasta] w/ index no sizes") {
test("Bacteroides fragilis genome [fasta] w/ index - keep dots") {
when {

params {
Expand All @@ -67,6 +69,7 @@ nextflow_workflow {
)
input[1] = false
input[2] = true
input[3] = true
"""
}

Expand All @@ -77,6 +80,45 @@ nextflow_workflow {
{ assert workflow.success },
{ assert snapshot(
path(workflow.out.dict[0][1]).readLines()[0],
path(workflow.out.reference[0][1]).readLines()[0],
workflow.out.reference,
workflow.out.fai,
workflow.out.sizes,
workflow.out.sequence_description
).match() }
)
}
}

test("Bacteroides fragilis genome [fasta] w/ index no sizes") {
when {

params {
outdir = "test"
}

workflow {
"""
input[0] = channel.of(
[
[ id: 'test' ],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
)
input[1] = true
input[2] = false
input[3] = true
"""
}

}

then {
assertAll(
{ assert workflow.success },
{ assert snapshot(
path(workflow.out.dict[0][1]).readLines()[0],
path(workflow.out.reference[0][1]).readLines()[0],
workflow.out.reference,
workflow.out.fai,
workflow.out.sequence_description
Expand All @@ -99,8 +141,9 @@ nextflow_workflow {
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true)
]
)
input[1] = false
input[1] = true
input[2] = false
input[3] = false
"""
}

Expand Down Expand Up @@ -132,6 +175,7 @@ nextflow_workflow {
)
input[1] = true
input[2] = true
input[3] = true
"""
}
}
Expand Down
57 changes: 51 additions & 6 deletions subworkflows/nf-core/fasta_clean_faidx/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,7 +1,51 @@
{
"Bacteroides fragilis genome [fasta] w/ index - keep dots": {
"content": [
"@HD\tVN:1.0\tSO:unsorted",
">NZ_CP069563.1",
[
[
{
"id": "test"
},
"test.fasta:md5,96aa7707b864499745e8946f169ae8e0"
]
],
[
[
{
"id": "test"
},
"test.fasta.fai:md5,f1373ef38f3777bcf9567be2e1f5c468"
]
],
[
[
{
"id": "test"
},
"test.fasta.sizes:md5,acc65893c145aa8385e4afb4f4662623"
]
],
[
[
{
"id": "test"
},
"test.json:md5,1e536d080509f7fc34114f0bc58a514d"
]
]
],
"timestamp": "2026-08-28T17:29:22.581741203",
"meta": {
"nf-test": "0.9.5",
"nextflow": "25.04.6"
}
},
"Bacteroides fragilis genome [fasta] w/ index": {
"content": [
"@HD\tVN:1.0\tSO:unsorted",
">NZ_CP069563_1",
[
[
{
Expand Down Expand Up @@ -35,10 +79,10 @@
]
]
],
"timestamp": "2026-08-26T10:00:11.358890143",
"timestamp": "2026-08-28T12:57:01.005284326",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
"nextflow": "25.04.6"
}
},
"Bacteroides fragilis genome - stub": {
Expand Down Expand Up @@ -148,15 +192,16 @@
]
}
],
"timestamp": "2026-08-26T10:00:31.191958515",
"timestamp": "2026-08-28T17:29:42.76692073",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
"nextflow": "25.04.6"
}
},
"Bacteroides fragilis genome [fasta] w/ index no sizes": {
"content": [
"@HD\tVN:1.0\tSO:unsorted",
">NZ_CP069563_1",
[
[
{
Expand All @@ -182,10 +227,10 @@
]
]
],
"timestamp": "2026-08-26T10:00:21.054412137",
"timestamp": "2026-08-28T17:29:32.864768835",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
"nextflow": "25.04.6"
}
}
}