From 4e0137f111e130797e97431d5e62a9deb51e6a0c Mon Sep 17 00:00:00 2001
From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Date: Tue, 25 Mar 2025 12:11:54 +0100
Subject: [PATCH 1/5] Update encrypted software

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index af786995..97ba06ea 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -123,10 +123,10 @@ jobs:
 
       - name: Install non-free software
         env:
-          DECRYPT_PASSPHRASE: ${{ secrets.TEST_NETMHC }}
+          DECRYPT_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}
         run: |
           mkdir -v non-free
-          curl -L https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/non-free-software.tar.gpg | ${GITHUB_WORKSPACE}/bin/decrypt | tar -C non-free -v -x
+          curl -L https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/netMHCpan-4.1b.Linux.tar.gz.gpg | ${GITHUB_WORKSPACE}/bin/decrypt | tar -C non-free -v -x
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

From d8a82e71092337acb5b2295d4a5667fa732cab19 Mon Sep 17 00:00:00 2001
From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Date: Tue, 25 Mar 2025 12:13:31 +0100
Subject: [PATCH 2/5] Update test_netmhcpan.config

---
 conf/test_netmhcpan.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test_netmhcpan.config b/conf/test_netmhcpan.config
index 931aae36..7244e3ac 100644
--- a/conf/test_netmhcpan.config
+++ b/conf/test_netmhcpan.config
@@ -21,7 +21,7 @@ params {
 
     input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
     tools = 'netmhcpan'
-    netmhcpan_path = './non-free/netmhcpan.tar.gz'
+    netmhcpan_path = './non-free/netMHCpan-4.1b.Linux.tar.gz'
     // Reduce number of possible peptide lengths to speed up test
     min_peptide_length_classI = 9
     max_peptide_length_classI = 10

From 52a91f4256d0ff5093c7a9ef7872a31990d8c7c9 Mon Sep 17 00:00:00 2001
From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Date: Tue, 25 Mar 2025 14:57:39 +0100
Subject: [PATCH 3/5] Update ci.yml

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 97ba06ea..296df063 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -125,8 +125,8 @@ jobs:
         env:
           DECRYPT_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}
         run: |
-          mkdir -v non-free
-          curl -L https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/netMHCpan-4.1b.Linux.tar.gz.gpg | ${GITHUB_WORKSPACE}/bin/decrypt | tar -C non-free -v -x
+          curl -L -o netMHCpan-4.1b.Linux.tar.gz.gpg https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/software/netMHCpan-4.1b.Linux.tar.gz.gpg
+          gpg --batch --yes --pinentry-mode=loopback --passphrase "${{ secrets.GPG_PASSPHRASE }}" --output ${GITHUB_WORKSPACE}/netMHCpan-4.1b.Linux.tar.gz --decrypt netMHCpan-4.1b.Linux.tar.gz.gpg
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

From c12a76381cbc1c3e24a3b473c466fa430683e11d Mon Sep 17 00:00:00 2001
From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Date: Tue, 25 Mar 2025 15:49:18 +0100
Subject: [PATCH 4/5] Update test_netmhcpan.config

---
 conf/test_netmhcpan.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/test_netmhcpan.config b/conf/test_netmhcpan.config
index 7244e3ac..7df5939c 100644
--- a/conf/test_netmhcpan.config
+++ b/conf/test_netmhcpan.config
@@ -21,7 +21,7 @@ params {
 
     input  = params.pipelines_testdata_base_path + 'epitopeprediction/testdata/sample_sheets/sample_sheet_peptides.csv'
     tools = 'netmhcpan'
-    netmhcpan_path = './non-free/netMHCpan-4.1b.Linux.tar.gz'
+    netmhcpan_path = './netMHCpan-4.1b.Linux.tar.gz'
     // Reduce number of possible peptide lengths to speed up test
     min_peptide_length_classI = 9
     max_peptide_length_classI = 10

From 5e7d448e0e3467606e4f4847cb94d4940026925c Mon Sep 17 00:00:00 2001
From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Date: Tue, 25 Mar 2025 20:57:26 +0100
Subject: [PATCH 5/5] Delete bin/decrypt

---
 bin/decrypt | 10 ----------
 1 file changed, 10 deletions(-)
 delete mode 100755 bin/decrypt

diff --git a/bin/decrypt b/bin/decrypt
deleted file mode 100755
index 61c15b3a..00000000
--- a/bin/decrypt
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/sh
-# Decrypts stdin -> stdout reading the passphrase from the environment variable
-# DECRYPT_PASSPHRASE.
-gpg \
-    --quiet \
-    --batch \
-    --yes \
-    --decrypt \
-    --passphrase="$DECRYPT_PASSPHRASE" \
-    --output -