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bam_taps_conversion: optional rastair version 2 caller (use_rastair2) #13641

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Merged
eduard-watchmaker merged 9 commits into from
Nov 11, 2026
Merged

bam_taps_conversion: optional rastair version 2 caller (use_rastair2) #13641

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6dd8bc9
bam_taps_conversion: add use_rastair2 option
eduard-watchmaker Nov 9, 2026
e7c031f
rastair2/mbias: new module; rastair2/call: take M-bias cutoffs
eduard-watchmaker Nov 10, 2026
e571a6f
Merge branch 'rastair2-mbias' into bam-taps-conversion-rastair2
eduard-watchmaker Nov 10, 2026
f4278b9
bam_taps_conversion: trim rastair2 calls with rastair2/mbias cutoffs
eduard-watchmaker Nov 10, 2026
5526975
rastair2/mbias, rastair2/call: lowercase channel, named closure param…
eduard-watchmaker Nov 10, 2026
401e2d9
Merge branch 'rastair2-mbias' into bam-taps-conversion-rastair2
eduard-watchmaker Nov 10, 2026
71f130e
rastair2/mbias: no estimate instead of an error when no read has a CpG
eduard-watchmaker Nov 10, 2026
68b65a2
Merge branch 'rastair2-mbias' into bam-taps-conversion-rastair2
eduard-watchmaker Nov 10, 2026
5c337cb
bam_taps_conversion: optional trims input to replace the M-bias estimate
eduard-watchmaker Nov 10, 2026
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9 changes: 8 additions & 1 deletion modules/nf-core/rastair2/call/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ process RASTAIR2_CALL {
: 'community.wave.seqera.io/library/htslib_rastair:4ffd26b40813e268'}"

input:
tuple val(meta), path(bam), path(index)
tuple val(meta), path(bam), path(index), path(mbias_cutoffs)
tuple val(meta2), path(fasta), path(fai)

output:
Expand All @@ -27,10 +27,17 @@ process RASTAIR2_CALL {
def prefix = task.ext.prefix ?: "${meta.id}"
// Single-end reads carry no pairing flags: strand comes from the alignment direction alone.
def unpaired = meta.single_end ? '--unpaired' : ''
// Bases to ignore at read ends, as suggested by rastair2/mbias: line 1 is --nOT, line 2 --nOB
def cutoffs_files = mbias_cutoffs instanceof List ? mbias_cutoffs : [mbias_cutoffs]
if (cutoffs_files.size() > 1) {
error("rastair2/call takes one M-bias cutoffs file per sample, got ${cutoffs_files.size()}: restrict rastair2/mbias to one contig with --region")
}
def trim = cutoffs_files ? "--nOT \$(sed -n 1p ${mbias_cutoffs}) --nOB \$(sed -n 2p ${mbias_cutoffs})" : ''
"""
rastair call \\
${args} \\
${unpaired} \\
${trim} \\
--threads ${task.cpus} \\
--fasta-file ${fasta} \\
--vcf ${prefix}.vcf.gz \\
Expand Down
9 changes: 9 additions & 0 deletions modules/nf-core/rastair2/call/meta.yml
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Expand Up @@ -51,6 +51,15 @@ input:
pattern: "*.{bai,csi,crai}"
ontologies:
- edam: "http://edamontology.org/format_3327"
- mbias_cutoffs:
type: file
description: |
Optional. One M-bias cutoffs file from rastair2/mbias (pass `[]` for none).
Line 1 is used as `--nOT` and line 2 as `--nOB`: bases to ignore at the
read ends, as `r1_start,r1_end,r2_start,r2_end`.
pattern: "*.cutoffs.txt"
ontologies:
- edam: "http://edamontology.org/format_3475"
- - meta2:
type: map
description: |
Expand Down
103 changes: 81 additions & 22 deletions modules/nf-core/rastair2/call/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ nextflow_process {
tag "modules_nfcore"
tag "rastair2"
tag "rastair2/call"
tag "rastair2/mbias"

// NOTE The VCF header records the command line (including --threads), so only the #CHROM line
// and records are snapshotted. They are hashed as text because rastair declares Number=M
Expand All @@ -18,12 +19,13 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end:false ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
[]
])
input[1] = Channel.of([
input[1] = channel.of([
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
Expand All @@ -33,11 +35,11 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert path(process.out.vcf[0][1]).linesGzip.any { it.startsWith('##rastairVersion=') } },
{ assert path(process.out.vcf[0][1]).linesGzip.any { line -> line.startsWith('##rastairVersion=') } },
{ assert snapshot(
path(process.out.vcf[0][1]).linesGzip.findAll { !it.startsWith('##') }.join('\n').md5(),
path(process.out.vcf[0][1]).linesGzip.findAll { line -> !line.startsWith('##') }.join('\n').md5(),
process.out.tbi.collect { meta, tbi -> file(tbi).name },
process.out.bed,
process.out.bed_tbi.collect { meta, tbi -> file(tbi).name },
Expand All @@ -52,12 +54,13 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end:true ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true),
[]
])
input[1] = Channel.of([
input[1] = channel.of([
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
Expand All @@ -67,11 +70,11 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert path(process.out.vcf[0][1]).linesGzip.any { it.startsWith('##rastairCommand=') && it.contains('--unpaired') } },
{ assert path(process.out.vcf[0][1]).linesGzip.any { line -> line.startsWith('##rastairCommand=') && line.contains('--unpaired') } },
{ assert snapshot(
path(process.out.vcf[0][1]).linesGzip.findAll { !it.startsWith('##') }.join('\n').md5(),
path(process.out.vcf[0][1]).linesGzip.findAll { line -> !line.startsWith('##') }.join('\n').md5(),
process.out.tbi.collect { meta, tbi -> file(tbi).name },
process.out.bed,
process.out.bed_tbi.collect { meta, tbi -> file(tbi).name },
Expand All @@ -86,12 +89,13 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end:false ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true),
[]
])
input[1] = Channel.of([
input[1] = channel.of([
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
Expand All @@ -101,11 +105,65 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert path(process.out.vcf[0][1]).linesGzip.any { !it.startsWith('#') } },
{ assert path(process.out.vcf[0][1]).linesGzip.any { line -> !line.startsWith('#') } },
{ assert snapshot(
path(process.out.vcf[0][1]).linesGzip.findAll { !it.startsWith('##') }.join('\n').md5(),
path(process.out.vcf[0][1]).linesGzip.findAll { line -> !line.startsWith('##') }.join('\n').md5(),
process.out.tbi.collect { meta, tbi -> file(tbi).name },
process.out.bed,
process.out.bed_tbi.collect { meta, tbi -> file(tbi).name },
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
}

test("sarscov2 - paired-end methylated bam - mbias cutoffs") {

setup {
run("RASTAIR2_MBIAS") {
script "../../mbias/main.nf"
process {
"""
input[0] = channel.of([
[ id:'test', single_end:false ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
])
input[1] = channel.of([
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
])
"""
}
}
}

when {
process {
"""
input[0] = channel.of([
[ id:'test', single_end:false ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
]).join(RASTAIR2_MBIAS.out.cutoffs)
input[1] = channel.of([
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
])
"""
}
}

then {
assert process.success
assertAll(
{ assert path(process.out.vcf[0][1]).linesGzip.any { line -> line.startsWith('##rastairCommand=') && line.contains('--nOT') && line.contains('--nOB') } },
{ assert snapshot(
path(process.out.vcf[0][1]).linesGzip.findAll { line -> !line.startsWith('##') }.join('\n').md5(),
process.out.tbi.collect { meta, tbi -> file(tbi).name },
process.out.bed,
process.out.bed_tbi.collect { meta, tbi -> file(tbi).name },
Expand All @@ -122,12 +180,13 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of([
input[0] = channel.of([
[ id:'test', single_end:false ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
[]
])
input[1] = Channel.of([
input[1] = channel.of([
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
Expand All @@ -137,8 +196,8 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
Expand Down
41 changes: 41 additions & 0 deletions modules/nf-core/rastair2/call/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,47 @@
"nextflow": "26.10.5"
}
},
"sarscov2 - paired-end methylated bam - mbias cutoffs": {
"content": [
"d1630262a4ab6255e9e441e6857e746f",
[
"test.vcf.gz.tbi"
],
[
[
{
"id": "test",
"single_end": false
},
"test.bed.gz:md5,ed8237adc7795a7485dab20c69146675"
]
],
[
"test.bed.gz.tbi"
],
{
"versions_rastair": [
[
"RASTAIR2_CALL",
"rastair",
"2.2.0"
]
],
"versions_tabix": [
[
"RASTAIR2_CALL",
"tabix",
"1.24"
]
]
}
],
"timestamp": "2026-11-10T10:58:57.116513",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.10.5"
}
},
"sarscov2 - single-end bam": {
"content": [
"1b3f2f0fde4de41a51853252c8ba063f",
Expand Down
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