Fix NETMHCSTABANDPAN to support samples without SV data

[johnoooh]

Description

Fixes a silent failure in the NETMHCSTABANDPAN subworkflow when samples are run without structural variants — a common case in MSK pipelines where the samplesheet only carries MAF/HLA/CNV inputs.

Root cause

createNETMHCInput joins ch_fasta_and_hla against ch_sv_fasta with an inner .join(...). When no SV files are provided in the samplesheet, the upstream NEOSV process never runs, so the SV fasta channel emits zero items. The inner join therefore produces an empty channel, and NETMHCSTABPAN / NETMHCPAN4 / NEOANTIGENUTILS_FORMATNETMHCPAN — and everything downstream of them in any pipeline using this subworkflow — silently get skipped.

Existing tests cover the case where the SV channel emits [meta, [], []] (empty file lists with a meta), but not the "no items at all" case, which is what real pipelines hit when SVs aren't part of the sample.

Change

Switch the join to a left join with remainder: true and treat a missing SV side as [null, [], []], so a MUT and WT tuple is still emitted per sample regardless of SV presence:

def merged_mut = fastas_and_hla_channel
    .join(sv_fastas_channel, by:0, remainder: true)
    .map({
        def sv = it[2] ?: [null, [], []]
        [it[1][0], it[1][1], sv[1], it[1][3], "MUT"]
    })

Tests

Adds netmhcstabandpan - empty SV channel - fa,hla_str - tsv - stub, which feeds input[1] = channel.empty() to lock in the SV-less code path.

All 7 tests pass locally (Nextflow 24.10.6, nf-test 0.9.5):

Test [f411820f] 'netmhcstabandpan - SV - fa,hla_str - tsv'                                 PASSED
Test [474d8bcb] 'netmhcstabandnetmhc3 - SV - fa,hla_str - tsv'                             PASSED
Test [f20bb7d2] 'netmhcstabandpan - fa,hla_str - tsv'                                      PASSED
Test [b2d766c9] 'netmhcstabandnetmhc3 - fa,hla_str - tsv'                                  PASSED
Test [958a9bbe] 'netmhcstabandpan - empty SV channel - fa,hla_str - tsv - stub'  (NEW)     PASSED
Test [d1dc7b0c] 'netmhcstabandpan - fa,hla_str - tsv - stub'                               PASSED
Test [1be0a66d] 'netmhcstabandnetmhc3 - fa,hla_str - tsv - stub'                           PASSED

The fix was also verified end-to-end by running the mskcc/neoantigenpipeline (-profile test,docker): before the fix the pipeline silently completed with 6 of 13 stages skipped after GENERATEMUTFASTA; after the fix all 31 processes run to completion (0 failures), producing the final TSV and annotated JSON outputs.

PR Checklist

• Description of changes with reasoning
• No nf-core equivalent (MSK-specific netMHC stack)
• Branch named feature/netmhcstabandpan
• Tests added for new code (regression test for empty SV channel)
• No external test data needed (stub-mode test)
• No TODOs introduced
• versions.yml emission untouched
• Naming conventions followed
• No resource label changes
• No container changes

[pintoa1-mskcc]

Good for our purposes, if we ever plan on using this in clinical production we would need to output empty files in cases like this, rather than skipping the step