Duplicate level of "neoantigen" directory in "Result folder"

[gongyixiao]

Below two lines result in duplicated level of neoantigen directory in the "Result" folder when publishing the result

https://github.com/mskcc/vaporware/blob/bfc446dc16336802790e6644f37e1e9f0cc32fd8/pipeline.nf#L1470

https://github.com/mskcc/vaporware/blob/bfc446dc16336802790e6644f37e1e9f0cc32fd8/pipeline.nf#L1489

Current directory structure looks like:

    ├── neoantigen
    │   └── neoantigen
    │       ├── neoantigen_run.log
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.all_neoantigen_predictions.txt
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.mutated_sequences.debug.fa
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.mutated_sequences.fa
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.neoantigens.maf
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.netmhc4.output.txt
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.netmhc4.output.xls
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.netmhcpan4.output.txt
    │       ├── s_C_000029_T001_d_vs_s_C_000029_N001_d.netmhcpan4.output.xls
    │       └── s_C_000029_T001_d_vs_s_C_000029_N001_d.netmhcpan_netmhc_combined.output.txt

[evanbiederstedt]

The awkwardness is a bit due to how the neoantigen script was written, and it was fit into NF.

We could try https://github.com/mskcc/vaporware/blob/master/pipeline.nf#L1467-L1470

process RunNeoantigen {
  tag {idTumor + "_vs_" + idNormal}

  publishDir "${params.outDir}/${idTumor}_vs_${idNormal}/somatic_variants", mode: params.publishDirMode

and that should resolve this.

I'll double-check this works: https://github.com/mskcc/vaporware/pull/469