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Stream NETMHCSTABANDPAN per sample instead of waiting on full SV channel #247

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262bc0f
Stream NETMHCSTABANDPAN per sample instead of waiting on full SV channel
johnoooh May 26, 2026
f8e7239
Update empty-SV regression test for new pre-pad contract
johnoooh May 27, 2026
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20 changes: 14 additions & 6 deletions subworkflows/msk/generate_mutated_peptides/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -56,24 +56,29 @@ workflow GENERATE_MUTATED_PEPTIDES {

ch_versions = ch_versions.mix(GENERATEMUTFASTA.out.versions)

ch_neosv_input = createNEOSVInput( ch_sv , NEOANTIGENUTILS_GENERATEHLASTRING.out.hlastring )
ch_neosv_branched = branchNEOSVInput( ch_sv , NEOANTIGENUTILS_GENERATEHLASTRING.out.hlastring )

NEOSV( ch_neosv_input, ch_gtf_and_cdna )
NEOSV( ch_neosv_branched.with_sv, ch_gtf_and_cdna )

ch_versions = ch_versions.mix(NEOSV.out.versions)

// Pad SV outputs with empty placeholders for samples without SV input so that
// downstream per-sample joins never have to wait for the full channel to close.
ch_sv_mut_fasta = NEOSV.out.mutOut.mix( ch_neosv_branched.without_sv.map{ [it[0], []] } )
ch_sv_wt_fasta = NEOSV.out.wtOut.mix( ch_neosv_branched.without_sv.map{ [it[0], []] } )

emit:

mut_fasta = GENERATEMUTFASTA.out.mut_fasta // channel: [ val(meta), [ *.MUT_sequences.fa ] ]
wt_fasta = GENERATEMUTFASTA.out.wt_fasta // channel: [ val(meta), [ *.WT_sequences.fa ] ]
mut_fasta_log = GENERATEMUTFASTA.out.mut_fasta_log // channel: [ val(meta), [ *_generate_mut_fasta.log ] ]
sv_mut_fasta = NEOSV.out.mutOut // channel: [ val(meta), [ *.SV.MUT.fa ] ]
sv_wt_fasta = NEOSV.out.wtOut // channel: [ val(meta), [ *.SV.WT.fa ] ]
sv_mut_fasta = ch_sv_mut_fasta // channel: [ val(meta), [ *.SV.MUT.fa ] | [] ]
sv_wt_fasta = ch_sv_wt_fasta // channel: [ val(meta), [ *.SV.WT.fa ] | [] ]
hla_string = NEOANTIGENUTILS_GENERATEHLASTRING.out.hlastring // channel: [ val(meta), [ hla_string ] ]
versions = ch_versions // channel: [ versions.yml ]
}

def createNEOSVInput(sv_bedpe, hla_str) {
def branchNEOSVInput(sv_bedpe, hla_str) {
def sv_bedpe_channel = sv_bedpe
.map{
[it[0],it]
Expand All @@ -89,6 +94,9 @@ def createNEOSVInput(sv_bedpe, hla_str) {
.map{
[it[1][0], it[1][1], it[2][1]]
}
.filter{ it[1] != null && it[2] != null }
.branch{
with_sv: it[1] != null && it[2] != null
without_sv: true
}
return merged_sv_hla
}
14 changes: 7 additions & 7 deletions subworkflows/msk/netmhcstabandpan/main.nf
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Expand Up @@ -58,19 +58,19 @@ def createNETMHCInput(fastas_and_hla, sv_fastas) {
[it[0],it]
}

// remainder: true keeps samples that have no SV data (sv_fastas is empty when no SVs provided)
// Callers are expected to pre-pad sv_fastas with [meta, []] for samples without SV data,
// so this is a plain inner join — each sample emits as soon as its fastas are ready and
// we never have to wait for the SV channel to close.
def merged_mut = fastas_and_hla_channel
.join(sv_fastas_channel, by:0, remainder: true)
.join(sv_fastas_channel, by:0)
.map({
def sv = it[2] ?: [null, [], []]
[it[1][0], it[1][1], sv[1], it[1][3], "MUT"]
[it[1][0], it[1][1], it[2][1], it[1][3], "MUT"]
})

def merged_wt = fastas_and_hla_channel
.join(sv_fastas_channel, by:0, remainder: true)
.join(sv_fastas_channel, by:0)
.map({
def sv = it[2] ?: [null, [], []]
[it[1][0], it[1][2], sv[2], it[1][3], "WT"]
[it[1][0], it[1][2], it[2][2], it[1][3], "WT"]
})
def merged = merged_mut.mix(merged_wt)
return merged
Expand Down
21 changes: 15 additions & 6 deletions subworkflows/msk/netmhcstabandpan/tests/main.nf.test
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Expand Up @@ -162,11 +162,12 @@ nextflow_workflow {
}


test("netmhcstabandpan - empty SV channel - fa,hla_str - tsv - stub") {
test("netmhcstabandpan - padded empty SV placeholder - fa,hla_str - tsv - stub") {

// Regression test: when no SV files are provided, the upstream NEOSV process
// doesn't run, so the sv_fasta channel emits zero items. The createNETMHCInput
// helper must still emit MUT and WT tuples for each sample.
// Regression test for the per-sample streaming contract:
// when a sample has no SV data, callers (e.g. GENERATE_MUTATED_PEPTIDES)
// pad the SV channel with [meta, [], []] so every sample matches the
// inner join. The subworkflow must still emit per-sample tsv outputs.

options "-stub"

Expand All @@ -180,7 +181,11 @@ nextflow_workflow {
"HLA-A24:02,HLA-A24:02,HLA-B39:01,HLA-B39:01,HLA-C07:01,HLA-C06:02",
])

input[1] = channel.empty()
input[1] = channel.value([
[ id:'test', single_end:false ], // meta map
[],
[]
])
"""
}
}
Expand All @@ -191,7 +196,11 @@ nextflow_workflow {
{ assert snapshot(workflow.out.tsv[0][0],
file(workflow.out.tsv[0][1]).name,
workflow.out.tsv[1][0],
file(workflow.out.tsv[1][1]).name
file(workflow.out.tsv[1][1]).name,
workflow.out.tsv[2][0],
file(workflow.out.tsv[2][1]).name,
workflow.out.tsv[3][0],
file(workflow.out.tsv[3][1]).name
).match()
}
)
Expand Down
22 changes: 19 additions & 3 deletions subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap
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Expand Up @@ -213,7 +213,7 @@
},
"timestamp": "2025-12-19T14:22:41.854041255"
},
"netmhcstabandpan - empty SV channel - fa,hla_str - tsv - stub": {
"netmhcstabandpan - padded empty SV placeholder - fa,hla_str - tsv - stub": {
"content": [
{
"id": "test",
Expand All @@ -230,12 +230,28 @@
"fromStab": true,
"typePan": true
},
"test.WT.STAB.tsv"
"test.WT.STAB.tsv",
{
"id": "test",
"single_end": false,
"typeMut": true,
"fromStab": false,
"typePan": true
},
"test.MUT.PAN.tsv",
{
"id": "test",
"single_end": false,
"typeMut": true,
"fromStab": true,
"typePan": true
},
"test.MUT.STAB.tsv"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2026-05-13T22:29:19.315483"
"timestamp": "2026-05-27T16:15:00.000000000"
}
}
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