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Update to use bioawk #216

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e742ac4
Update to use bioawk
DLBPointon Mar 26, 2026
3b42e6f
Spelling mistake in file path
DLBPointon Mar 26, 2026
9643ab3
Merge branch 'main' into telo_fix
DLBPointon Mar 26, 2026
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38 changes: 31 additions & 7 deletions subworkflows/sanger-tol/telo_finder/main.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
//
// MODULE IMPORT BLOCK
//
include { BIOAWK } from '../../../modules/nf-core/bioawk/main'
include { TELOMERE_REGIONS } from '../../../modules/sanger-tol/telomere/regions/main'
include { GAWK as GAWK_SPLIT_TELOMERE } from '../../../modules/nf-core/gawk/main'
include { TELOMERE_WINDOWS } from '../../../modules/sanger-tol/telomere/windows/main'
Expand All @@ -12,20 +13,42 @@ workflow TELO_FINDER {

take:
ch_reference // Channel [ val(meta), path(fasta) ]
ch_telomereseq // Channel.of( telomere sequence )
ch_telomereseq // Channel [ val(meta), path(fasta) ]
val_split_telomere // bool
val_run_bgzip // bool

main:

//if G > 30% then flip else pass
//
// MODULE: BIOAWK CONVERT THE MOTIF INTO THE 5 PRIME DIRECTION
// IF PROVIDED IN THE 3 PRIME DIRECTION
// IF MOTIF HAS A G CONTENT OF > 30% IT IS IN THE 3 PRIME
//
BIOAWK(
ch_telomereseq,
"tsv"
)


//
// LOGIC: READ LINE 2 OF THE OUTPUT FILE
//
corrected_telomere = BIOAWK.out.output
.map { _meta, file ->
def lines = file.toFile().readLines()
// Lines from bioawk are:
// corrected_sequence G_count G_percentage reversed? original_sequence
lines[0].split('\t')[0]
}
.filter { it != null }

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@prototaxites prototaxites Mar 26, 2026

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Should this keep meta in the output? When would it return null and what should the behaviour be in this case?

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@DLBPointon DLBPointon Mar 26, 2026

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in all fairness there should never be a null. If there's a null you've forgotten to include a telomere and will have other issues.


//
// MODULE: FINDS THE TELOMERIC SEQEUNCE IN REFERENCE
//
TELOMERE_REGIONS (
ch_reference,
ch_telomereseq
corrected_telomere
)

ch_full_telomere = TELOMERE_REGIONS.out.telomere
Expand Down Expand Up @@ -89,7 +112,7 @@ workflow TELO_FINDER {
// THIS ONLY HAPPENS ON WHOLE TELOMERIC FILES
//
TELOMERE_WINDOWS (
ch_regions_for_extraction.filter { meta, file -> meta.direction == 0 }
ch_regions_for_extraction.filter { meta, _file -> meta.direction == 0 }
)

//
Expand Down Expand Up @@ -140,8 +163,9 @@ workflow TELO_FINDER {
)

emit:
bed_file = ch_telo_bedfiles // Channel [meta, bed]
bed_gz_tbi = TABIX_BGZIPTABIX.out.gz_index // Not used anymore
bedgraph_file = ch_telo_bedgraphs // Channel [meta, [bedfiles]] - Used in pretext_graph
telomere_summary = BIOAWK.out.output // Channel [meta, tsv]
bed_file = ch_telo_bedfiles // Channel [meta, bed]
bed_gz_tbi = TABIX_BGZIPTABIX.out.gz_index // Channel [meta, index]
bedgraph_file = ch_telo_bedgraphs // Channel [meta, [bedfiles]] - Used in pretext_graph

}
11 changes: 10 additions & 1 deletion subworkflows/sanger-tol/telo_finder/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@ components:
- telomere/regions
- telomere/windows
- telomere/extract
- bioawk:
git_remote: https://github.com/nf-core/modules.git
- gawk:
git_remote: https://github.com/nf-core/modules.git
- tabix/bgziptabix:
Expand All @@ -23,8 +25,10 @@ input:
Meta is the Groovy Map containing sample information
Reference is the fasta for analysis
- ch_telomereseq:
type: string
type: file
description: |
Structure [ val(meta), path(reference) ]
Meta is the Groovy Map containing sample information
A string containing the DNA sequence of a telomere motif
- val_split_telomere:
type: boolean
Expand All @@ -35,6 +39,11 @@ input:
description: |
Control running of tabix with boolean
output:
- telomere_summary:
type: file
description: |
Structure: [ val(meta), path(tsv) ]
A tsv file summarising the telomere regions found.
- bed_file:
type: file
description: |
Expand Down
5 changes: 5 additions & 0 deletions subworkflows/sanger-tol/telo_finder/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
nextflow.enable.moduleBinaries = true

process {

withName: BIOAWK {
ext.args = { "-c fastx \'{s = toupper($seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct < 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\t%d\t%.2f\t%s\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s }\'" }
}
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@prototaxites prototaxites Mar 26, 2026

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One last question, very much optional, and which could have been prompted when you were doing the BIOAWK module before 😅 - would it be worth making the bioawk module more like the GAWK module and be able to take a program file? Then you could write this as a value channel in the subworkflow script?

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@DLBPointon DLBPointon Mar 26, 2026 •
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I did think about that, it would definately clean it up. But chose the path of least resistance.

I don't know if it can take a file as input to be honest, I'll mock up a test and get back to you.

Edit: actually right in the help line -f progfile

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@prototaxites prototaxites Mar 26, 2026

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I checked the bioawk command itself, it does also have the -f option to take an AWK program file.

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@DLBPointon DLBPointon Mar 26, 2026

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Yeah looks good:

dp24@tol22-head1:[0c/80f5275761405e54eaf6864f57b83d] (telo_fix):$: bioawk -c fastx -f cli.awk telomere_motif.fasta

CCTAA	2	40.00	true	TTAGG

I'll open up the modules repo again

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@DLBPointon DLBPointon Mar 26, 2026 •
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Rip it apart @prototaxites !
nf-core/modules#11060


withName: TELOMERE_WINDOWS {
tag = { "${meta.id}_${meta.direction}P" }
ext.args = "99.9"
Expand Down
35 changes: 29 additions & 6 deletions subworkflows/sanger-tol/telo_finder/tests/main.nf.test
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Expand Up @@ -12,10 +12,12 @@ nextflow_workflow {
tag "telomere/windows"
tag "telomere/extract"
tag "tabix/bgziptabix"
tag "subworkflows/../../modules/nf-core/bioawk"
tag "subworkflows/../../modules/nf-core/gawk"
tag "subworkflows/../../modules/nf-core/gunzip"
tag "subworkflows/../../modules/nf-core/tabix/bgziptabix"
tag "modules/nf-core/gunzip"
tag "modules/nf-core/bioawk"

setup {
nfcoreInitialise("${launchDir}/library/")
Expand All @@ -24,7 +26,8 @@ nextflow_workflow {
[
"gawk",
"tabix/bgziptabix",
"gunzip"
"gunzip",
"bioawk"
]
)
nfcoreLink("${launchDir}/library/", "${baseDir}/modules/")
Expand All @@ -46,14 +49,18 @@ nextflow_workflow {
test("idFanCani4 - no split - fasta w/ index") {
when {
params {
bioawk_command = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct > 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\\t%d\\t%.2f\\t%s\\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s }\'"
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@yumisims yumisims Mar 26, 2026

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The benefit is that json could be reused in other workflows, but thinking about it, this should already be sufficient.

windows_percent = "99.9"
bgzip_args = "--csi"
}

workflow {
"""
input[0] = GUNZIP.out.gunzip
input[1] = "TTAGG"
input[1] = [
[ id: "motifs" ],
file(params.modules_testdata_base_path + 'resources/modules/telomere/generic/telomere_motif.fasta', checkIfExists: true)
]
input[2] = false
input[3] = true
"""
Expand All @@ -75,14 +82,18 @@ nextflow_workflow {
test("idFanCani4 - split - fasta w/ index") {
when {
params {
bioawk_command = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct > 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\\t%d\\t%.2f\\t%s\\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s }\'"
windows_percent = "99.9"
bgzip_args = "--csi"
}

workflow {
"""
input[0] = GUNZIP.out.gunzip
input[1] = "TTAGG"
input[1] = [
[ id: "motifs" ],
file(params.modules_testdata_base_path + 'resources/modules/telomere/generic/telomere_motif.fasta', checkIfExists: true)
]
input[2] = true
input[3] = true
"""
Expand All @@ -104,14 +115,18 @@ nextflow_workflow {
test("idFanCani4 - no split - fasta w/o index") {
when {
params {
bioawk_command = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct > 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\\t%d\\t%.2f\\t%s\\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s }\'"
windows_percent = "99.9"
bgzip_args = "--csi"
}

workflow {
"""
input[0] = GUNZIP.out.gunzip
input[1] = "TTAGG"
input[1] = [
[ id: "motifs" ],
file(params.modules_testdata_base_path + 'resources/modules/telomere/generic/telomere_motif.fasta', checkIfExists: true)
]
input[2] = false
input[3] = false
"""
Expand All @@ -133,14 +148,18 @@ nextflow_workflow {
test("idFanCani4 - split - fasta w/o index") {
when {
params {
bioawk_command = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct > 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\\t%d\\t%.2f\\t%s\\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s }\'"
windows_percent = "99.9"
bgzip_args = "--csi"
}

workflow {
"""
input[0] = GUNZIP.out.gunzip
input[1] = "TTAGG"
input[1] = [
[ id: "motifs" ],
file(params.modules_testdata_base_path + 'resources/modules/telomere/generic/telomere_motif.fasta', checkIfExists: true)
]
input[2] = true
input[3] = false
"""
Expand All @@ -162,14 +181,18 @@ nextflow_workflow {
test("idFanCani4 - no split - fasta - stub w/o index") {
when {
params {
bioawk_command = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct > 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\\t%d\\t%.2f\\t%s\\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s }\'"
windows_percent = "99.9"
bgzip_args = "--csi"
}

workflow {
"""
input[0] = GUNZIP.out.gunzip
input[1] = "TTAGG"
input[1] = [
[ id: "motifs" ],
file(params.modules_testdata_base_path + 'resources/modules/telomere/generic/telomere_motif.fasta', checkIfExists: true)
]
input[2] = false
input[3] = false
"""
Expand Down
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