Add CI tests for NetMHC family tools

.github/workflows/ci.yml

@@ -89,3 +89,53 @@ jobs:
         - name: Run pipeline with profile ${{ matrix.tests }}
           run: |
             nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker
+
+  nonfree:
+      name: Run non-free tests
+      if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/epitopeprediction') }}
+      runs-on: ubuntu-latest
+      env:
+        NXF_VER: '20.04.0'
+        NXF_ANSI_LOG: false
+      steps:
+        - name: Check out pipeline code
+          uses: actions/checkout@v2
+
+        - name: Install non-free software
+          env:
+            DECRYPT_PASSPHRASE: ${{ secrets.TEST_NETMHC }}
+          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
+
+        - name: Check if Dockerfile or Conda environment changed
+          uses: technote-space/get-diff-action@v4
+          with:
+            FILES: |
+              Dockerfile
+              environment.yml
+        - name: Build new docker image
+          if: env.MATCHED_FILES
+          run: docker build --no-cache . -t nfcore/epitopeprediction:dev
+
+        - name: Pull docker image
+          if: ${{ !env.MATCHED_FILES }}
+          run: |
+            docker pull nfcore/epitopeprediction:dev
+            docker tag nfcore/epitopeprediction:dev nfcore/epitopeprediction:dev
+        - name: Install Nextflow
+          run: |
+            wget -qO- get.nextflow.io | bash
+            sudo mv nextflow /usr/local/bin/
+        - 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

bin/decrypt

@@ -0,0 +1,10 @@
+#!/bin/sh
+# Decrypts stdin -> stdout reading the passphrase from the environment variable
+# DECRYPT_PASSPHRASE.
+gpg \
+	--quiet \
+	--batch \
+	--yes \
+	--decrypt \
+	--passphrase="$DECRYPT_PASSPHRASE" \
+	--output -

conf/test_netmhc.config

@@ -0,0 +1,24 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/epitopeprediction -profile test_netmhc,<docker/singularity>
+ */
+
+params {
+  config_profile_name = 'NetMHC Test Profile'
+  config_profile_description = 'Peptide list based test profile for NetMHC'
+
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+
+  // Input data
+  peptides = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/peptides/peptides.tsv'
+  alleles = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/alleles/alleles.txt'
+
+  tools = 'netmhc'
+  netmhc_path = './non-free/netmhc.tar.gz'
+}

conf/test_netmhcii.config

@@ -0,0 +1,24 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/epitopeprediction -profile test_netmhcii,<docker/singularity>
+ */
+
+params {
+  config_profile_name = 'NetMHCII Test Profile'
+  config_profile_description = 'Peptide list based test profile for NetMHCII'
+
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+
+  // Input data
+  peptides = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/peptides/peptides_MHC_II.txt'
+  alleles = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/alleles/alleles.DRB1_01_01.txt'
+
+  tools = 'netmhcii'
+  netmhcii_path = './non-free/netmhcii.tar.Z'
+}

conf/test_netmhciipan.config

@@ -0,0 +1,24 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/epitopeprediction -profile test_netmhciipan,<docker/singularity>
+ */
+
+params {
+  config_profile_name = 'NetMHCIIpan Test Profile'
+  config_profile_description = 'Peptide list based test profile for NetMHCIIpan'
+
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+
+  // Input data
+  peptides = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/peptides/peptides_MHC_II.txt'
+  alleles = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/alleles/alleles.DRB1_01_01.txt'
+
+  tools = 'netmhciipan'
+  netmhciipan_path = './non-free/netmhciipan.tar.gz'
+}

conf/test_netmhcpan.config

@@ -0,0 +1,24 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run nf-core/epitopeprediction -profile test_netmhcpan,<docker/singularity>
+ */
+
+params {
+  config_profile_name = 'NetMHCpan Test Profile'
+  config_profile_description = 'Peptide list based test profile for NetMHCpan'
+
+  max_cpus = 2
+  max_memory = 6.GB
+  max_time = 48.h
+
+  // Input data
+  peptides = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/peptides/peptides.tsv'
+  alleles = 'https://raw.githubusercontent.com/nf-core/test-datasets/epitopeprediction/testdata/alleles/alleles.txt'
+
+  tools = 'netmhcpan'
+  netmhcpan_path = './non-free/netmhcpan.tar.gz'
+}

nextflow.config

@@ -99,6 +99,10 @@ profiles {
   test_proteins { includeConfig 'conf/test_proteins.config' }
   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' }
 }