diff --git a/modules/msk/neoantigenutils/formatnetmhcpan/tests/main.nf.test.snap b/modules/msk/neoantigenutils/formatnetmhcpan/tests/main.nf.test.snap index f821cd31..b84f7d60 100644 --- a/modules/msk/neoantigenutils/formatnetmhcpan/tests/main.nf.test.snap +++ b/modules/msk/neoantigenutils/formatnetmhcpan/tests/main.nf.test.snap @@ -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": [ @@ -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": [ @@ -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": [ @@ -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": [ @@ -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": [ @@ -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": [ @@ -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" } } \ No newline at end of file diff --git a/modules/msk/netmhc3/main.nf b/modules/msk/netmhc3/main.nf index 8a4c013d..42ec13d5 100644 --- a/modules/msk/netmhc3/main.nf +++ b/modules/msk/netmhc3/main.nf @@ -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 diff --git a/modules/msk/netmhc3/tests/main.nf.test.snap b/modules/msk/netmhc3/tests/main.nf.test.snap index ac230cbb..ae10569b 100644 --- a/modules/msk/netmhc3/tests/main.nf.test.snap +++ b/modules/msk/netmhc3/tests/main.nf.test.snap @@ -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": [ @@ -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": [ @@ -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": [ @@ -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": [ @@ -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" } } \ No newline at end of file diff --git a/modules/msk/netmhcpan4/main.nf b/modules/msk/netmhcpan4/main.nf index d6c603f6..4533d57a 100644 --- a/modules/msk/netmhcpan4/main.nf +++ b/modules/msk/netmhcpan4/main.nf @@ -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 diff --git a/modules/msk/netmhcpan4/tests/main.nf.test.snap b/modules/msk/netmhcpan4/tests/main.nf.test.snap index fa054ef2..e345b825 100644 --- a/modules/msk/netmhcpan4/tests/main.nf.test.snap +++ b/modules/msk/netmhcpan4/tests/main.nf.test.snap @@ -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": [ @@ -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": [ @@ -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": [ @@ -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": [ @@ -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" } } \ No newline at end of file diff --git a/modules/msk/netmhcstabpan/main.nf b/modules/msk/netmhcstabpan/main.nf index da1dce34..114c1062 100644 --- a/modules/msk/netmhcstabpan/main.nf +++ b/modules/msk/netmhcstabpan/main.nf @@ -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" diff --git a/modules/msk/netmhcstabpan/tests/main.nf.test.snap b/modules/msk/netmhcstabpan/tests/main.nf.test.snap index eda2c922..b99a46db 100644 --- a/modules/msk/netmhcstabpan/tests/main.nf.test.snap +++ b/modules/msk/netmhcstabpan/tests/main.nf.test.snap @@ -9,15 +9,15 @@ "single_end": false, "typeMut": true, "fromStab": true, - "typePan": true + "fromPan": true }, "test.MUT.netmhcstabpan.output" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-11-25T09:20:13.007454444" + "timestamp": "2024-12-17T13:19:10.187818681" }, "netmhcstabpan - WT,SV - xls,output,fa": { "content": [ @@ -29,15 +29,15 @@ "single_end": false, "typeMut": false, "fromStab": true, - "typePan": true + "fromPan": true }, "test.WT.netmhcstabpan.output" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-11-25T09:15:21.840510308" + "timestamp": "2024-12-17T13:15:25.815673176" }, "netmhcstabpan - xls,output,fa - stub": { "content": [ @@ -54,10 +54,10 @@ "test.MUT.netmhcstabpan.output" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-11-25T09:25:26.180428087" + "timestamp": "2024-12-17T13:23:26.483556017" }, "netmhcstabpan - WT - xls,output,fa": { "content": [ @@ -69,15 +69,15 @@ "single_end": false, "typeMut": false, "fromStab": true, - "typePan": true + "fromPan": true }, "test.WT.netmhcstabpan.output" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-11-25T09:25:21.015015849" + "timestamp": "2024-12-17T13:23:16.341803658" }, "netmhcstabpan - MUT,SV - xls,output,fa": { "content": [ @@ -89,14 +89,14 @@ "single_end": false, "typeMut": true, "fromStab": true, - "typePan": true + "fromPan": true }, "test.MUT.netmhcstabpan.output" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-11-25T09:09:53.461848085" + "timestamp": "2024-12-17T13:11:09.443476183" } } \ No newline at end of file diff --git a/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap index b77b94a1..aeeee539 100644 --- a/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap +++ b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap @@ -1,15 +1,15 @@ { "netmhcstabandpan - tsv,xls,fa": { "content": [ - "test_netmhc.output.WT.tsv", + "test_netmhcpan.output.WT.tsv", "test.MUT_sequences.fa:md5,7fdb7d3f0fe5a6f439ed294b612c2d70", "test.WT_sequences.fa:md5,7595ed6cf0c98500b00c9ad027125b38" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-12-02T17:16:20.890584183" + "timestamp": "2024-12-17T15:32:48.122038795" }, "netmhcstabandpan - tsv,xls,fa - stub": { "content": [ @@ -18,10 +18,10 @@ "test.WT_sequences.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-12-02T17:17:10.765080369" + "timestamp": "2024-12-17T15:33:59.951435808" }, "netmhcstabandnetmhc3 - SV - tsv,xls,fa": { "content": [ @@ -30,22 +30,22 @@ "test.WT_sequences.fa:md5,bb7dfff23ae47cf64ec4854ee48ec78d" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-12-02T17:15:41.011763441" + "timestamp": "2024-12-17T15:31:41.007610492" }, "netmhcstabandpan - SV - tsv,xls,fa": { "content": [ - "test_netmhc.output.WT.tsv", + "test_netmhcpan.output.WT.tsv", "test.MUT_sequences.fa:md5,118b48df96c7217675b9f9ac14309a25", "test.WT_sequences.fa:md5,bb7dfff23ae47cf64ec4854ee48ec78d" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-12-02T17:14:23.137692552" + "timestamp": "2024-12-17T15:29:06.330489514" }, "netmhcstabandnetmhc3 - tsv,xls,fa": { "content": [ @@ -54,9 +54,9 @@ "test.WT_sequences.fa:md5,7595ed6cf0c98500b00c9ad027125b38" ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-12-02T17:17:01.585453593" + "timestamp": "2024-12-17T15:33:45.014740679" } } \ No newline at end of file