From 9666ad0612bd356e9e094efd48c1fb2b54e4198d Mon Sep 17 00:00:00 2001
From: Christopher Mohr <christopher.mohr@uni-tuebingen.de>
Date: Wed, 15 Dec 2021 18:12:33 +0100
Subject: [PATCH] Remove netmhcii specs and deactivate corresponding tests

---
 .github/workflows/ci.yml       |  6 ------
 nextflow.config                |  2 --
 workflows/epitopeprediction.nf | 16 +---------------
 3 files changed, 1 insertion(+), 23 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3c5906d..52dbd3e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -125,12 +125,6 @@ jobs:
       - name: Run pipeline with NetMHC
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_netmhc,docker
-      - name: Run pipeline with NetMHCII
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_netmhcii,docker
       - name: Run pipeline with NetMHCpan
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_netmhcpan,docker
-      - name: Run pipeline with NetMHCIIpan
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_netmhciipan,docker
diff --git a/nextflow.config b/nextflow.config
index 7cd8164..974b282 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -140,9 +140,7 @@ profiles {
     test_mhcnuggets { includeConfig 'conf/test_mhcnuggets.config' }
     test_mhcflurry { includeConfig 'conf/test_mhcflurry.config' }
     test_netmhc { includeConfig 'conf/test_netmhc.config' }
-    test_netmhcii { includeConfig 'conf/test_netmhcii.config' }
     test_netmhcpan { includeConfig 'conf/test_netmhcpan.config' }
-    test_netmhciipan { includeConfig 'conf/test_netmhciipan.config' }
     test_full { includeConfig 'conf/test_full.config' }
 }
 
diff --git a/workflows/epitopeprediction.nf b/workflows/epitopeprediction.nf
index 0152897..a9aed37 100644
--- a/workflows/epitopeprediction.nf
+++ b/workflows/epitopeprediction.nf
@@ -128,20 +128,6 @@ workflow EPITOPEPREDICTION {
             data_url     : "https://services.healthtech.dtu.dk/services/NetMHCpan-4.0/data.Linux.tar.gz",
             data_md5     : "26cbbd99a38f6692249442aeca48608f",
             binary_name  : "netMHCpan"
-        ],
-        netmhcii: [
-            version      : "2.2",
-            software_md5 : "918b7108a37599887b0725623d0974e6",
-            data_url     : "https://services.healthtech.dtu.dk/services/NetMHCII-2.2/data.tar.gz",
-            data_md5     : "11579b61d3bfe13311f7b42fc93b4dd8",
-            binary_name  : "netMHCII"
-        ],
-        netmhciipan: [
-            version      : "3.1",
-            software_md5 : "0962ce799f7a4c9631f8566a55237073",
-            data_url     : "https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.1/data.tar.gz",
-            data_md5     : "f833df245378e60ca6e55748344a36f6",
-            binary_name  : "netMHCIIpan"
         ]
     ]
 
@@ -224,7 +210,7 @@ workflow EPITOPEPREDICTION {
     }
 
     // Retrieve meta data for external tools
-    ["netmhc", "netmhcpan", "netmhcii", "netmhciipan"].each {
+    ["netmhc", "netmhcpan"].each {
         // Check if the _path parameter was set for this tool
         if (params["${it}_path"] as Boolean && ! tools.contains(it))
         {