Merge pull request #124 from mskcc-omics-workflows/feature/neosv

Feature/neosv
mskcc-omics-workflows · Aug 29, 2024 · 4da70f0 · 4da70f0
2 parents 0b5126b + b1d45c0
commit 4da70f0
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Showing 26 changed files with 766 additions and 225 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -416,6 +416,8 @@ jobs:
             tags: salmon/quant
           - profile: "conda"
             tags: rediscoverte
+          - profile: "conda"
+            tags: neosv
 
     env:
       NXF_ANSI_LOG: false

diff --git a/modules/msk/neoantigenutils/formatnetmhcpan/meta.yml b/modules/msk/neoantigenutils/formatnetmhcpan/meta.yml
@@ -38,6 +38,7 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+
   - netMHCpanreformatted:
       type: file
       description: A reformatted file of neoantigens and their binding affinities output by netmhcpan or netmhcstabpan.  This contains the wild type antigens

diff --git a/modules/msk/neoantigenutils/formatnetmhcpan/tests/main.nf.test.snap b/modules/msk/neoantigenutils/formatnetmhcpan/tests/main.nf.test.snap
@@ -9,7 +9,7 @@
                             "typeMut": true,
                             "fromStab": false
                         },
-                        "test_netmHCpanoutput.MUT.tsv:md5,7f00f2df190fe801700b626b72dfdb99"
+                        "test_netmHCpanoutput.MUT.tsv:md5,26f40dde35f53f5ced8a251f59dcc77f"
                     ]
                 ],
                 "1": [
@@ -22,15 +22,19 @@
                             "typeMut": true,
                             "fromStab": false
                         },
-                        "test_netmHCpanoutput.MUT.tsv:md5,7f00f2df190fe801700b626b72dfdb99"
+                        "test_netmHCpanoutput.MUT.tsv:md5,26f40dde35f53f5ced8a251f59dcc77f"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,2c02f5f3103ee1532c27f7f3b873a578"
                 ]
             }
         ],
-        "timestamp": "2024-07-30T13:46:27.878268"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T15:37:30.153345025"
     },
     "neoantigenutils_formatnetmhcpan - output(MUT,netmhcpan) - tsv - stub": {
         "content": [
@@ -63,7 +67,11 @@
                 ]
             }
         ],
-        "timestamp": "2024-07-30T13:47:05.72509"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T15:38:06.423945648"
     },
     "neoantigenutils_formatnetmhcpan - output(WT,netmhcpan) - tsv": {
         "content": [
@@ -75,7 +83,7 @@
                             "typeMut": false,
                             "fromStab": false
                         },
-                        "test_netmHCpanoutput.WT.tsv:md5,a1d7db1b6f116e96457f2fa60660558e"
+                        "test_netmHCpanoutput.WT.tsv:md5,0ef95cf63ee0b8faa8e9d85413e48943"
                     ]
                 ],
                 "1": [
@@ -88,15 +96,19 @@
                             "typeMut": false,
                             "fromStab": false
                         },
-                        "test_netmHCpanoutput.WT.tsv:md5,a1d7db1b6f116e96457f2fa60660558e"
+                        "test_netmHCpanoutput.WT.tsv:md5,0ef95cf63ee0b8faa8e9d85413e48943"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,2c02f5f3103ee1532c27f7f3b873a578"
                 ]
             }
         ],
-        "timestamp": "2024-07-30T13:46:37.183992"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T15:37:39.559652073"
     },
     "neoantigenutils_formatnetmhcpan - output(MUT,netmhcpanstab) - tsv": {
         "content": [
@@ -129,7 +141,11 @@
                 ]
             }
         ],
-        "timestamp": "2024-07-30T13:46:47.110076"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T15:37:48.839508094"
     },
     "neoantigenutils_formatnetmhcpan - output(WT,netmhcpanstab) - tsv": {
         "content": [
@@ -162,6 +178,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-07-30T13:46:56.841519"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-21T15:37:57.894905711"
     }
 }
diff --git a/modules/msk/neoantigenutils/neoantigeninput/main.nf b/modules/msk/neoantigenutils/neoantigeninput/main.nf
@@ -6,7 +6,7 @@ process NEOANTIGENUTILS_NEOANTIGENINPUT {
         'docker.io/mskcc/neoantigen-utils-base:1.1.0' }"
 
     input:
-    tuple val(meta),  path(inputMaf),      path(hlaFile)
+    tuple val(meta),  path(inputMaf),      path(inputBedpe),    path(hlaFile)
     tuple val(meta2), path(phyloWGSsumm),  path(phyloWGSmut),   path(phyloWGSfolder)
     tuple val(meta3), path(mutNetMHCpan),  path(wtNetMHCpan)
 
@@ -33,13 +33,14 @@ process NEOANTIGENUTILS_NEOANTIGENINPUT {
 
 
         generate_input.py --maf_file ${inputMaf} \
+        --bedpe_file ${inputBedpe} \
         --summary_file ${id}.summ.json \
         --mutation_file ${id}.mut.json \
         --tree_directory \$tree_folder_name \
         --id ${id} --patient_id ${patientid} \
         --cohort ${cohort} --HLA_genes ${hlaFile} \
         --netMHCpan_MUT_input ${mutNetMHCpan} \
-        --netMHCpan_WT_input ${wtNetMHCpan}
+        --netMHCpan_WT_input ${wtNetMHCpan} \
         ${args}
 
 

diff --git a/modules/msk/neoantigenutils/neoantigeninput/meta.yml b/modules/msk/neoantigenutils/neoantigeninput/meta.yml
@@ -54,6 +54,11 @@ input:
       description: HLA tsv outputtted by Polysolver
       pattern: "winners.{tsv}"
 
+  - inputBedpe:
+      type: file
+      description: bedpe file containing SVs
+      pattern: "winners.{tsv}"
+
 output:
   - meta:
       type: map