From 6d723a440de85cbf8fd83725043f8f11e3739252 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 27 Nov 2024 15:00:23 +0000 Subject: [PATCH 01/17] Update CODEOWNERS file --- .github/CODEOWNERS | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 2508a98f..b6736d41 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -28,8 +28,8 @@ ./modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers ./modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers ./modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/quant/** @mskcc-omics-workflows/reviewers +./modules/msk/salmon/index/** @kevinmenden @drpatelh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/salmon/quant/** @kevinmenden @drpatelh @mskcc-omics-workflows/reviewers ./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers ./subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers ./subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers From 8de2653a47c455137f8ddd2d170f82e1e5bdcf2c Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 27 Nov 2024 15:04:42 +0000 Subject: [PATCH 02/17] Update CODEOWNERS file --- .github/CODEOWNERS | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index b6736d41..6947500f 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -28,8 +28,8 @@ ./modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers ./modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers ./modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/index/** @kevinmenden @drpatelh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/quant/** @kevinmenden @drpatelh @mskcc-omics-workflows/reviewers +./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers ./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers ./subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers ./subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers From b65cb67755136df6e6059df0765ca05a13e61ec7 Mon Sep 17 00:00:00 2001 From: John Orgera Date: Tue, 17 Dec 2024 09:31:05 -0500 Subject: [PATCH 03/17] typePan to fromPan --- modules/msk/netmhcpan4/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 9e23d0e98023dec8b7a9b0faa20eea2f1f9cee3f Mon Sep 17 00:00:00 2001 From: John Orgera Date: Tue, 17 Dec 2024 12:02:15 -0500 Subject: [PATCH 04/17] updated test --- .../msk/netmhcpan4/tests/main.nf.test.snap | 38 +++++++++---------- .../netmhcstabandpan/tests/main.nf.test.snap | 36 +++++++++--------- 2 files changed, 37 insertions(+), 37 deletions(-) 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/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap index 38a320df..b3c83712 100644 --- a/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap +++ b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap @@ -1,27 +1,27 @@ { "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": "2024-11-25T10:05:45.541764396" + "timestamp": "2024-12-17T11:05:29.465425713" }, "netmhcstabandpan - tsv,xls,fa - stub": { "content": [ - "h", + "j", "test.MUT_sequences.fa:md5,d41d8cd98f00b204e9800998ecf8427e", "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": "2024-11-25T10:06:34.087540628" + "timestamp": "2024-12-17T11:06:27.567900754" }, "netmhcstabandnetmhc3 - SV - tsv,xls,fa": { "content": [ @@ -30,22 +30,22 @@ "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": "2024-11-25T10:05:05.649074818" + "timestamp": "2024-12-17T11:04:24.11780427" }, "netmhcstabandpan - SV - tsv,xls,fa": { "content": [ - "test_netmhc.output.WT.tsv", + "test_netmhcpan.output.WT.tsv", "test.MUT_sequences.fa:md5,fc9a3f7760bc72beb0e74d1b851e80fd", "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": "2024-11-25T10:03:43.312026049" + "timestamp": "2024-12-17T11:01:41.788941356" }, "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": "2024-11-25T10:06:24.948690627" + "timestamp": "2024-12-17T11:06:13.800807658" } } \ No newline at end of file From 0ccb264740ff8fe681f0e298133e52e51bf68994 Mon Sep 17 00:00:00 2001 From: John Orgera Date: Tue, 17 Dec 2024 14:00:06 -0500 Subject: [PATCH 05/17] more tests and netmhc changes --- modules/msk/netmhc3/main.nf | 2 +- modules/msk/netmhc3/tests/main.nf.test.snap | 38 +++++++++---------- modules/msk/netmhcstabpan/main.nf | 2 +- .../msk/netmhcstabpan/tests/main.nf.test.snap | 38 +++++++++---------- 4 files changed, 40 insertions(+), 40 deletions(-) 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/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 From 5741a514d07fcb8e3782d00cceea51b1568bc6f2 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 17 Dec 2024 19:20:21 +0000 Subject: [PATCH 06/17] Update CODEOWNERS file --- .github/CODEOWNERS | 72 +++++++++++++++++++++++----------------------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 6947500f..08db581a 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -1,38 +1,38 @@ # Review from a member of the review-team is required * @mskcc-omics-workflows/reviewers -./modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers -./modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers -./modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers -./modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers -./modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers -./subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers -./subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers +modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers +modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers +modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers +modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers +subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers +subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers From 939507da8ef974fa8b9f53abd5f9d54492bafab0 Mon Sep 17 00:00:00 2001 From: John Orgera Date: Tue, 17 Dec 2024 15:11:06 -0500 Subject: [PATCH 07/17] fixed test --- .../formatnetmhcpan/tests/main.nf.test.snap | 42 +++++++++---------- 1 file changed, 21 insertions(+), 21 deletions(-) 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 From 848ad2b5cffd9a4bd15a628cfe59aba93807a252 Mon Sep 17 00:00:00 2001 From: John Orgera Date: Tue, 17 Dec 2024 15:47:29 -0500 Subject: [PATCH 08/17] new snap --- .../netmhcstabandpan/tests/main.nf.test.snap | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap index 99d6a0dc..aeeee539 100644 --- a/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap +++ b/subworkflows/msk/netmhcstabandpan/tests/main.nf.test.snap @@ -9,11 +9,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-12-17T11:05:29.465425713" + "timestamp": "2024-12-17T15:32:48.122038795" }, "netmhcstabandpan - tsv,xls,fa - stub": { "content": [ - "j", + "h", "test.MUT_sequences.fa:md5,d41d8cd98f00b204e9800998ecf8427e", "test.WT_sequences.fa:md5,d41d8cd98f00b204e9800998ecf8427e" ], @@ -21,7 +21,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-12-17T11:06:27.567900754" + "timestamp": "2024-12-17T15:33:59.951435808" }, "netmhcstabandnetmhc3 - SV - tsv,xls,fa": { "content": [ @@ -33,20 +33,19 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-12-17T11:04:24.11780427" + "timestamp": "2024-12-17T15:31:41.007610492" }, "netmhcstabandpan - SV - tsv,xls,fa": { "content": [ "test_netmhcpan.output.WT.tsv", - "test.MUT_sequences.fa:md5,fc9a3f7760bc72beb0e74d1b851e80fd", - "test.WT_sequences.fa:md5,7595ed6cf0c98500b00c9ad027125b38" - + "test.MUT_sequences.fa:md5,118b48df96c7217675b9f9ac14309a25", + "test.WT_sequences.fa:md5,bb7dfff23ae47cf64ec4854ee48ec78d" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-12-17T11:01:41.788941356" + "timestamp": "2024-12-17T15:29:06.330489514" }, "netmhcstabandnetmhc3 - tsv,xls,fa": { "content": [ @@ -58,6 +57,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-12-17T11:06:13.800807658" + "timestamp": "2024-12-17T15:33:45.014740679" } } \ No newline at end of file From c5bc9c3ce69ba21d3b353a4ba60061b7a52e63a5 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Wed, 18 Dec 2024 10:46:19 -0500 Subject: [PATCH 09/17] Update CODEOWNERS ./ added, maybe this will fix --- .github/CODEOWNERS | 72 +++++++++++++++++++++++----------------------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 08db581a..6947500f 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -1,38 +1,38 @@ # Review from a member of the review-team is required * @mskcc-omics-workflows/reviewers -modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers -modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers -modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers -modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers -modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers -modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers -modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers -modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers -subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers -subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers -subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers -subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers -subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers +./modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers +./modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers +./modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers +./modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers +./modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers +./modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers +./subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers +./subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers +./subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers +./subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers +./subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers From 4b324a339f6895f713c930c316b7f744f933d473 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 15:47:45 +0000 Subject: [PATCH 10/17] Update CODEOWNERS file --- .github/CODEOWNERS | 72 +++++++++++++++++++++++----------------------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 6947500f..08db581a 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -1,38 +1,38 @@ # Review from a member of the review-team is required * @mskcc-omics-workflows/reviewers -./modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers -./modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers -./modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers -./modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers -./modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers -./subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers -./subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers +modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers +modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers +modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers +modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers +subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers +subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers From 123b4dc8cef31932b179aba7fde73904149625de Mon Sep 17 00:00:00 2001 From: John Orgera Date: Wed, 18 Dec 2024 11:14:42 -0500 Subject: [PATCH 11/17] Version of nf-test changed. --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 912e55f6..14a292f6 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -448,7 +448,7 @@ jobs: - name: Install nf-test if: steps.cache-software.outputs.cache-hit != 'true' run: | - wget -qO- https://code.askimed.com/install/nf-test | bash + curl -fsSL https://get.nf-test.com | bash -s ${{NFTEST_VER}} sudo mv nf-test /usr/local/bin/ - name: Setup apptainer From df93119876a4ac9d06230fde00d6a60ce0fae2d1 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Wed, 18 Dec 2024 11:20:28 -0500 Subject: [PATCH 12/17] Update CODEOWNERS --- .github/CODEOWNERS | 62 +++++++++++++++++++++++----------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 08db581a..7b91d601 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -1,36 +1,36 @@ # Review from a member of the review-team is required * @mskcc-omics-workflows/reviewers -modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers -modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers -modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers -modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers -modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers -modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers -modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers -modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers -modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers -modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers +./modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers +./modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers +./modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers +./modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +./modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers +./modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers +./modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers +./modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers +./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers From 98cc40fed94f0d313c25b3088bd8abd9ce3ae773 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Wed, 18 Dec 2024 11:20:51 -0500 Subject: [PATCH 13/17] Update CODEOWNERS --- .github/CODEOWNERS | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 7b91d601..6947500f 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -31,8 +31,8 @@ ./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers ./modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers ./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers -subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers -subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers -subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers -subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers -subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers +./subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers +./subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers +./subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers +./subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers +./subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers From ddce0e43633ae9dbd4f371c3aee3e042499e9812 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 16:21:31 +0000 Subject: [PATCH 14/17] Update CODEOWNERS file --- .github/CODEOWNERS | 72 +++++++++++++++++++++++----------------------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 6947500f..08db581a 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -1,38 +1,38 @@ # Review from a member of the review-team is required * @mskcc-omics-workflows/reviewers -./modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers -./modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers -./modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers -./modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers -./modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers -./modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers -./modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers -./modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers -./subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers -./subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers -./subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers +modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers +modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers +modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhcpan4/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/netmhcstabpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/createinput/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/multievolve/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/parsecnvs/** @pintoa1-mskcc @mskcc-omics-workflows/reviewers +modules/msk/phylowgs/writeresults/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/polysolver/** @anoronh4 @mskcc-omics-workflows/reviewers +modules/msk/ppflagfixer/** @huyu335 @mskcc-omics-workflows/reviewers +modules/msk/pvmaf/concat/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/pvmaf/tagtraceback/** @buehlere @mskcc-omics-workflows/reviewers +modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers +modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers +subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers +subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/phylowgs/** @nikhil @mskcc-omics-workflows/reviewers +subworkflows/msk/traceback/** @buehlere @mskcc-omics-workflows/reviewers From f6e60ab05e900eb9cb6fbcf73e6600f96669f720 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Wed, 18 Dec 2024 11:23:25 -0500 Subject: [PATCH 15/17] Update test.yml --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 14a292f6..544899d4 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -448,7 +448,7 @@ jobs: - name: Install nf-test if: steps.cache-software.outputs.cache-hit != 'true' run: | - curl -fsSL https://get.nf-test.com | bash -s ${{NFTEST_VER}} + curl -fsSL https://get.nf-test.com | bash -s ${{ env.NFTEST_VER }} sudo mv nf-test /usr/local/bin/ - name: Setup apptainer From dc7b880fbd1de27e8178f5765b5b3827f0b342e3 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Wed, 18 Dec 2024 12:18:01 -0500 Subject: [PATCH 16/17] make singularity writable --- tests/config/nf-test.config | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index b79f2f21..179ec398 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -15,6 +15,7 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + singularity.runOptions = "--writable" } conda { conda.enabled = true From e25a9e2498b134a2dfbcd142e60faec91ee2b6de Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Wed, 18 Dec 2024 12:28:31 -0500 Subject: [PATCH 17/17] Update nf-test.config --- tests/config/nf-test.config | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config index 179ec398..b79f2f21 100644 --- a/tests/config/nf-test.config +++ b/tests/config/nf-test.config @@ -15,7 +15,6 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true - singularity.runOptions = "--writable" } conda { conda.enabled = true