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Merge pull request #172 from mskcc-omics-workflows/bugfix/netmhc_feat…
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…ure_names

Bugfix netmhc feature names
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@nikhil
nikhil authored Jan 15, 2025
2 parents a7ed589 + 4adaabe commit 1b68e50
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Showing 8 changed files with 98 additions and 98 deletions.
42 changes: 21 additions & 21 deletions modules/msk/neoantigenutils/formatnetmhcpan/tests/main.nf.test.snap
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Expand Up @@ -33,10 +33,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-22T17:15:16.841503839"
"timestamp": "2024-12-17T14:45:38.840591896"
},
"neoantigenutils_formatnetmhcpan - output(WT,netmhc) - tsv": {
"content": [
Expand Down Expand Up @@ -72,10 +72,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-22T17:15:34.581815855"
"timestamp": "2024-12-17T14:46:02.600939484"
},
"neoantigenutils_formatnetmhcpan - output(MUT,netmhcpan) - tsv - stub": {
"content": [
Expand Down Expand Up @@ -111,10 +111,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-22T17:15:51.298318927"
"timestamp": "2024-12-17T14:46:25.074173512"
},
"neoantigenutils_formatnetmhcpan - output(MUT,netmhc) - tsv": {
"content": [
Expand Down Expand Up @@ -150,10 +150,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-22T17:15:28.833554691"
"timestamp": "2024-12-17T14:45:55.288256594"
},
"neoantigenutils_formatnetmhcpan - output(WT,netmhcpan) - tsv": {
"content": [
Expand Down Expand Up @@ -189,10 +189,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-22T17:15:23.00992256"
"timestamp": "2024-12-17T14:45:47.34586791"
},
"neoantigenutils_formatnetmhcpan - output(MUT,netmhcpanstab) - tsv": {
"content": [
Expand Down Expand Up @@ -228,10 +228,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-22T17:15:40.122191248"
"timestamp": "2024-12-17T14:46:10.256554716"
},
"neoantigenutils_formatnetmhcpan - output(WT,netmhcpanstab) - tsv": {
"content": [
Expand Down Expand Up @@ -267,9 +267,9 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-22T17:15:45.911170919"
"timestamp": "2024-12-17T14:46:17.955083074"
}
}
2 changes: 1 addition & 1 deletion modules/msk/netmhc3/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ process NETMHC3 {
output_meta = meta.clone()
output_meta.typeMut = inputType == "MUT" ? true : false
output_meta.fromStab = false
output_meta.typePan = false
output_meta.fromPan = false
def NETMHC_VERSION = "3.4"
def tmpDir = "netmhc-tmp"
def tmpDirFullPath = "\$PWD/${tmpDir}/" // must set full path to tmp directories for netMHC and netMHCpan to work; for some reason doesn't work with /scratch, so putting them in the process workspace
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38 changes: 19 additions & 19 deletions modules/msk/netmhc3/tests/main.nf.test.snap
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Expand Up @@ -9,16 +9,16 @@
"single_end": false,
"typeMut": true,
"fromStab": false,
"typePan": false
"fromPan": false
},
"test.MUT.xls",
"test.MUT.netmhc.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T09:00:51.333935874"
"timestamp": "2024-12-17T12:08:28.261935482"
},
"netmhc3 - xls,output,fa - stub": {
"content": [
Expand All @@ -36,10 +36,10 @@
"test.MUT.netmhc.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T09:02:00.341675799"
"timestamp": "2024-12-17T12:09:30.886623638"
},
"netmhc3 - WT,SV - xls,output,fa": {
"content": [
Expand All @@ -51,16 +51,16 @@
"single_end": false,
"typeMut": false,
"fromStab": false,
"typePan": false
"fromPan": false
},
"test.WT.xls",
"test.WT.netmhc.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T09:01:14.49522341"
"timestamp": "2024-12-17T12:08:47.429513751"
},
"netmhc3 - WT - xls,output,fa": {
"content": [
Expand All @@ -72,16 +72,16 @@
"single_end": false,
"typeMut": false,
"fromStab": false,
"typePan": false
"fromPan": false
},
"test.WT.xls",
"test.WT.netmhc.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T09:01:55.331175249"
"timestamp": "2024-12-17T12:09:21.112597962"
},
"netmhc3 - MUT - xls,output,fa": {
"content": [
Expand All @@ -93,15 +93,15 @@
"single_end": false,
"typeMut": true,
"fromStab": false,
"typePan": false
"fromPan": false
},
"test.MUT.xls",
"test.MUT.netmhc.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T09:01:34.648692712"
"timestamp": "2024-12-17T12:09:04.393123362"
}
}
2 changes: 1 addition & 1 deletion modules/msk/netmhcpan4/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ process NETMHCPAN4 {
output_meta = meta.clone()
output_meta.typeMut = inputType == "MUT" ? true : false
output_meta.fromStab = false
output_meta.typePan = true
output_meta.fromPan = true
def NETMHCPAN_VERSION = "4.1"
def tmpDir = "netmhc-tmp"
def tmpDirFullPath = "\$PWD/${tmpDir}/" // must set full path to tmp directories for netMHC and netMHCpan to work; for some reason doesn't work with /scratch, so putting them in the process workspace
Expand Down
38 changes: 19 additions & 19 deletions modules/msk/netmhcpan4/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -9,16 +9,16 @@
"single_end": false,
"typeMut": false,
"fromStab": false,
"typePan": true
"fromPan": true
},
"test.WT.xls",
"test.WT.netmhcpan.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T10:29:28.616914826"
"timestamp": "2024-12-17T09:55:05.982792409"
},
"netmhcpan4 - MUT - xls,output,fa": {
"content": [
Expand All @@ -30,16 +30,16 @@
"single_end": false,
"typeMut": true,
"fromStab": false,
"typePan": true
"fromPan": true
},
"test.MUT.xls",
"test.MUT.netmhcpan.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T10:26:02.108432464"
"timestamp": "2024-12-17T09:50:25.440240126"
},
"netmhcpan4 - xls,output,fa - stub": {
"content": [
Expand All @@ -57,10 +57,10 @@
"test.MUT.netmhcpan.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T10:29:33.956254062"
"timestamp": "2024-12-17T09:55:12.561294254"
},
"netmhcpan4 - MUT,SV - xls,output,fa": {
"content": [
Expand All @@ -72,16 +72,16 @@
"single_end": false,
"typeMut": true,
"fromStab": false,
"typePan": true
"fromPan": true
},
"test.MUT.xls",
"test.MUT.netmhcpan.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T10:20:37.334041838"
"timestamp": "2024-12-17T09:42:24.952790532"
},
"netmhcpan4 - WT,SV - xls,output,fa": {
"content": [
Expand All @@ -93,15 +93,15 @@
"single_end": false,
"typeMut": false,
"fromStab": false,
"typePan": true
"fromPan": true
},
"test.WT.xls",
"test.WT.netmhcpan.output"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-11-25T10:24:39.739383639"
"timestamp": "2024-12-17T09:47:58.298355664"
}
}
2 changes: 1 addition & 1 deletion modules/msk/netmhcstabpan/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ process NETMHCSTABPAN {
output_meta = meta.clone()
output_meta.typeMut = inputType == "MUT" ? true : false
output_meta.fromStab = true
output_meta.typePan = true
output_meta.fromPan = true

def NETMHCPAN_VERSION = "4.1"
def NETMHCSTABPAN_VERSION = "1.0"
Expand Down
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