mskcc · nikhil · Mar 7, 2025 · Mar 6, 2025 · Mar 6, 2025 · Mar 6, 2025
diff --git a/conf/modules.config b/conf/modules.config
@@ -32,4 +32,8 @@ process {
     withName: 'NEOANTIGENUTILS_NEOANTIGENINPUT' {
         ext.args = "--kD_cutoff ${params.kd_cutoff}"
     }
+
+    withName: 'NEOANTIGENEDITING_COMPUTEFITNESS' {
+        ext.args = "--a_param ${params.compute_fitness_a} --k_param ${params.compute_fitness_k} --w_param ${params.compute_fitness_w}"
+    }
 }
diff --git a/conf/prod.config b/conf/prod.config
@@ -37,8 +37,12 @@ params {
     phylo_mcmc_samples = 2500
     phylo_num_chains = 15
     kd_cutoff = 500
+    compute_fitness_a = 22.897590714815188
+    compute_fitness_k = 1
+    compute_fitness_w = 0.22402192838740312
 
     iedbfasta = 'https://raw.githubusercontent.com/mskcc/NeoantigenEditing/refs/heads/main/data/iedb.fasta'
     cds = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cds.all.fa.gz'
     cdna = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cdna.all.fa.gz'
+    gtf = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.gtf.gz'
 }
diff --git a/conf/test.config b/conf/test.config
@@ -33,8 +33,12 @@ params {
     phylo_num_chains = 2
     netmhc3 = true
     kd_cutoff = 500
+    compute_fitness_a = 22.897590714815188
+    compute_fitness_k = 1
+    compute_fitness_w = 0.22402192838740312
 
     iedbfasta = 'https://raw.githubusercontent.com/mskcc-omics-workflows/test-datasets/neoantigen/neoantigen/neoantigenEditing/data/iedb.fasta'
     cds = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cds.all.fa.gz'
     cdna = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.cdna.all.fa.gz'
+    gtf = 'https://github.com/mskcc-omics-workflows/test-datasets/raw/neoantigen/neoantigen/Homo_sapiens.GRCh37.75.gtf.gz'
 }
diff --git a/modules.json b/modules.json
@@ -12,44 +12,39 @@
                     },
                     "neoantigenediting/computefitness": {
                         "branch": "develop",
-                        "git_sha": "05e49188ee9407e1b51dfb1a49d8b6133e9276bc",
+                        "git_sha": "6aee6083154c666798e779c0aeb305614f4dcdd3",
                         "installed_by": ["modules", "neoantigen_editing"]
                     },
                     "neoantigenutils/convertannotjson": {
                         "branch": "develop",
-                        "git_sha": "34505c4c67eabebab927561d3a8fca87c9efe788",
+                        "git_sha": "e8ae6eb203cb5a49f98cacd4734090c182ad5f44",
                         "installed_by": ["modules"]
                     },
                     "neoantigenutils/formatnetmhcpan": {
                         "branch": "develop",
-                        "git_sha": "939507da8ef974fa8b9f53abd5f9d54492bafab0",
+                        "git_sha": "84f51051ee6735fc9dc8eea733eb84a54dc350bc",
                         "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "neoantigenutils/generatehlastring": {
                         "branch": "develop",
-                        "git_sha": "34505c4c67eabebab927561d3a8fca87c9efe788",
+                        "git_sha": "84f51051ee6735fc9dc8eea733eb84a54dc350bc",
                         "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "neoantigenutils/generatemutfasta": {
                         "branch": "develop",
-                        "git_sha": "e6bbb12a2dc237b9ea18163e96dbe9d780ddce5f",
+                        "git_sha": "e8ae6eb203cb5a49f98cacd4734090c182ad5f44",
                         "installed_by": ["modules", "netmhcstabandpan"]
                     },
                     "neoantigenutils/neoantigeninput": {
                         "branch": "develop",
-                        "git_sha": "ba014f40a3aaccd6a78db44f62d697b77a790eb8",
+                        "git_sha": "8b8e8d28b628b6244f4539cc405f2561fd733967",
                         "installed_by": ["modules"]
                     },
                     "netmhc3": {
                         "branch": "develop",
-                        "git_sha": "0ccb264740ff8fe681f0e298133e52e51bf68994",
+                        "git_sha": "26ac6cb270844a72838220ca239a22fcbe7f71f2",
                         "installed_by": ["modules", "netmhcstabandpan"]
                     },
-                    "netmhcpan": {
-                        "branch": "main",
-                        "git_sha": "503abeb67260f060d8228221b07d743aa4180345",
-                        "installed_by": ["modules"]
-                    },
                     "netmhcpan4": {
                         "branch": "develop",
                         "git_sha": "9e23d0e98023dec8b7a9b0faa20eea2f1f9cee3f",
@@ -62,7 +57,7 @@
                     },
                     "phylowgs/createinput": {
                         "branch": "develop",
-                        "git_sha": "05e49188ee9407e1b51dfb1a49d8b6133e9276bc",
+                        "git_sha": "e8ae6eb203cb5a49f98cacd4734090c182ad5f44",
                         "installed_by": ["phylowgs"]
                     },
                     "phylowgs/multievolve": {
@@ -86,12 +81,12 @@
                 "msk": {
                     "neoantigen_editing": {
                         "branch": "develop",
-                        "git_sha": "56a628201401866096d6307b9e8c690c5eb46ac2",
+                        "git_sha": "3284d77f55f0ef756d9ccd0519826fd7edd7d2ec",
                         "installed_by": ["subworkflows"]
                     },
                     "netmhcstabandpan": {
                         "branch": "develop",
-                        "git_sha": "848ad2b5cffd9a4bd15a628cfe59aba93807a252",
+                        "git_sha": "e8ae6eb203cb5a49f98cacd4734090c182ad5f44",
                         "installed_by": ["subworkflows"]
                     },
                     "phylowgs": {

diff --git a/modules/msk/neoantigenediting/computefitness/main.nf b/modules/msk/neoantigenediting/computefitness/main.nf
@@ -23,8 +23,8 @@ process NEOANTIGENEDITING_COMPUTEFITNESS {
     """
     compute_fitness.py \\
         --alignment ${alignment_file} \\
-        --input ${patient_data}
-
+        --input ${patient_data} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/msk/neoantigenediting/computefitness/resources/usr/bin/compute_fitness.py b/modules/msk/neoantigenediting/computefitness/resources/usr/bin/compute_fitness.py
@@ -285,19 +285,23 @@ def clean_data(tree):
 
     """
 
-    a = 22.897590714815188
-    k = 1
-    w = 0.22402192838740312
-
     parser = argparse.ArgumentParser(prog="align_neoantigens_to_IEDB")
     parser.add_argument("--alignment", help="neoantigen alignment file", required=True)
     parser.add_argument("--input", help="patient_data file", required=True)
-
+    parser.add_argument("--a_param", help="weight corresponding to a", default = 22.897590714815188)
+    parser.add_argument("--k_param", help="weight corresponding to k", default = 1)
+    parser.add_argument("--w_param", help="weight corresponding to w", default = 0.22402192838740312)
+
     args = parser.parse_args()
 
     alignment_file = args.alignment
     patient_file = args.input
 
+    a = float(args.a_param)
+    k = float(args.k_param)
+    w = float(args.w_param)
+
+
     epidist = EpitopeDistance()
 
     sample_file = patient_file

diff --git a/modules/msk/neoantigenediting/computefitness/tests/main.nf.test b/modules/msk/neoantigenediting/computefitness/tests/main.nf.test
@@ -3,6 +3,7 @@ nextflow_process {
     name "Test Process NEOANTIGENEDITING_COMPUTEFITNESS"
     script "../main.nf"
     process "NEOANTIGENEDITING_COMPUTEFITNESS"
+    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -20,6 +21,12 @@ nextflow_process {
                     file(params.test_data_mskcc['neoantigen']['patient_data'], checkIfExists: true),
                     file(params.test_data_mskcc['neoantigen']['iedb_alignments'], checkIfExists: true)
                     ]
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map,
+                    file(params.test_data_mskcc['neoantigen']['patient_data'], checkIfExists: true),
+                    file(params.test_data_mskcc['neoantigen']['iedb_alignments'], checkIfExists: true)
+                    ]
+
 
                 """
             }

diff --git a/modules/msk/neoantigenediting/computefitness/tests/nextflow.config b/modules/msk/neoantigenediting/computefitness/tests/nextflow.config
@@ -0,0 +1,9 @@
+params {
+    enable_conda = false
+}
+
+process {
+    withName: 'NEOANTIGENEDITING_COMPUTEFITNESS' {
+        ext.args = '--a_param 22.897590714815188 --k_param 1 --w_param 0.22402192838740312'
+    }
+}
diff --git a/modules/msk/neoantigenutils/convertannotjson/main.nf b/modules/msk/neoantigenutils/convertannotjson/main.nf
@@ -2,8 +2,8 @@ process NEOANTIGENUTILS_CONVERTANNOTJSON {
     tag "$meta.id"
     label 'process_single'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://mskcc/neoantigen-utils-base:1.0.0':
-        'docker.io/mskcc/neoantigen-utils-base:1.0.0' }"
+        'docker://mskcc/neoantigen-utils-base:1.3.0':
+        'docker.io/mskcc/neoantigen-utils-base:1.3.0' }"
 
     input:
     tuple val(meta),  path(annotatedJSON)

diff --git a/modules/msk/neoantigenutils/convertannotjson/resources/usr/bin/convertannotjson.py b/modules/msk/neoantigenutils/convertannotjson/resources/usr/bin/convertannotjson.py
@@ -3,38 +3,61 @@
 import json
 import argparse
 
-VERSION = 1.0
+VERSION = 1.1
 
-def process_json_file(json_file_path,output_file_path):
+
+def process_json_file(json_file_path, output_file_path):
     with open(json_file_path, "r") as json_file:
         data = json.load(json_file)
 
     # Define the TSV header
-    tsv_header = ["id", "mutation_id", "HLA_gene_id", "sequence", "WT_sequence", "mutated_position", "Kd", "KdWT", "R", "logC", "logA", "quality", "git_branch"]
+    tsv_header = [
+        "id",
+        "mutation_id",
+        "Gene",
+        "HLA_gene_id",
+        "sequence",
+        "WT_sequence",
+        "mutated_position",
+        "Kd",
+        "KdWT",
+        "R",
+        "logC",
+        "logA",
+        "quality",
+        "NMD",
+        "git_branch",
+    ]
 
     # Convert JSON to TSV
     tsv_lines = []
     tsv_lines.append("\t".join(tsv_header))
 
     for neoantigen in data["neoantigens"]:
-        tsv_lines.append("\t".join(str(neoantigen.get(field, "")) for field in tsv_header[:-1]))
+        tsv_lines.append(
+            "\t".join(str(neoantigen.get(field, "")) for field in tsv_header[:-1])
+        )
 
     tsv_output = "\n".join(tsv_lines)
 
     # Write the TSV output to a file
     with open(output_file_path, "w") as tsv_file:
         tsv_file.write(tsv_output)
 
+
 def main():
-    parser = argparse.ArgumentParser(description="Process an annotated JSON file and output TSV format.")
+    parser = argparse.ArgumentParser(
+        description="Process an annotated JSON file and output TSV format."
+    )
     parser.add_argument("--json_file", help="Path to the annotated JSON file")
     parser.add_argument("--output_file", help="Path to the output TSV file")
     parser.add_argument(
         "-v", "--version", action="version", version="v{}".format(VERSION)
     )
     args = parser.parse_args()
 
-    process_json_file(args.json_file,args.output_file)
+    process_json_file(args.json_file, args.output_file)
+
 
 if __name__ == "__main__":
     main()
diff --git a/modules/msk/neoantigenutils/convertannotjson/tests/main.nf.test.snap b/modules/msk/neoantigenutils/convertannotjson/tests/main.nf.test.snap
@@ -7,30 +7,30 @@
                         {
                             "id": "test"
                         },
-                        "test_neoantigens.tsv:md5,4931fb72bba8bbeb3bc6cef19b99b01a"
+                        "test_neoantigens.tsv:md5,38705f1ccbbeb9298037beb871e2e87c"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e36ea44c5cc6130f40b1a100f7e84fb1"
+                    "versions.yml:md5,07818f514d7f8471de49a39923d6921e"
                 ],
                 "neoantigenTSV": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_neoantigens.tsv:md5,4931fb72bba8bbeb3bc6cef19b99b01a"
+                        "test_neoantigens.tsv:md5,38705f1ccbbeb9298037beb871e2e87c"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e36ea44c5cc6130f40b1a100f7e84fb1"
+                    "versions.yml:md5,07818f514d7f8471de49a39923d6921e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-07-24T16:49:37.133693"
+        "timestamp": "2025-03-03T15:54:28.541430188"
     },
     "neoantigenutils_convertannotjson - output(test) - tsv - stub": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e36ea44c5cc6130f40b1a100f7e84fb1"
+                    "versions.yml:md5,07818f514d7f8471de49a39923d6921e"
                 ],
                 "neoantigenTSV": [
                     [
@@ -55,14 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e36ea44c5cc6130f40b1a100f7e84fb1"
+                    "versions.yml:md5,07818f514d7f8471de49a39923d6921e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-07-24T16:49:41.629164"
+        "timestamp": "2025-03-03T15:40:34.220309133"
     }
 }
diff --git a/modules/msk/neoantigenutils/formatnetmhcpan/main.nf b/modules/msk/neoantigenutils/formatnetmhcpan/main.nf
@@ -2,8 +2,8 @@ process NEOANTIGENUTILS_FORMATNETMHCPAN {
     tag "$meta.id"
     label 'process_single'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://mskcc/neoantigen-utils-base:1.0.0':
-        'docker.io/mskcc/neoantigen-utils-base:1.0.0' }"
+        'docker://mskcc/neoantigen-utils-base:1.3.0':
+        'docker.io/mskcc/neoantigen-utils-base:1.3.0' }"
 
     input:
     tuple val(meta),  path(netmhcPanOutput)

diff --git a/modules/msk/neoantigenutils/formatnetmhcpan/resources/usr/bin/format_netmhcpan_output.py b/modules/msk/neoantigenutils/formatnetmhcpan/resources/usr/bin/format_netmhcpan_output.py
@@ -46,7 +46,7 @@ def netMHCpan_out_reformat(netMHCoutput, mut, stab, netmhc3, prefix):
     if netmhc3:
         pan_prefix = ""
     outfilename = "{}_netmhc{}{}.output.{}.tsv".format(
-        prefix, pan_prefix, stab_prefix, type_prefix
+        prefix, stab_prefix, pan_prefix, type_prefix
     )
     with open(netMHCoutput, "r") as file:
         # data = file.read()