Add support for the non-free netMHC tool family

.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

CHANGELOG.md

@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.2.0dev
 
+### `Added`
+
+- [#73](https://github.com/nf-core/epitopeprediction/pull/73) - Add support for the non-free netmhc tool family
+
 ## v1.1.0 - Morgenstelle - 2020-10-20
 
 ### `Added`

README.md

@@ -45,7 +45,7 @@ The nf-core/epitopeprediction pipeline comes with documentation about the pipeli
 
 ## Credits
 
-nf-core/epitopeprediction was originally written by [Christopher Mohr](https://github.com/christopher-mohr) from [Institute for Translational Bioinformatics](https://kohlbacherlab.org/team_tbi/) and [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/) and [Alexander Peltzer](https://github.com/apeltzer) from [Böhringer Ingelheim](https://www.boehringer-ingelheim.de). Further contributions were made by [Sabrina Krakau](https://github.com/skrakau) from [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/).
+nf-core/epitopeprediction was originally written by [Christopher Mohr](https://github.com/christopher-mohr) from [Institute for Translational Bioinformatics](https://kohlbacherlab.org/team_tbi/) and [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/) and [Alexander Peltzer](https://github.com/apeltzer) from [Böhringer Ingelheim](https://www.boehringer-ingelheim.de). Further contributions were made by [Sabrina Krakau](https://github.com/skrakau) from [Quantitative Biology Center](https://uni-tuebingen.de/forschung/forschungsinfrastruktur/zentrum-fuer-quantitative-biologie-qbic/) and [Leon Kuchenbecker](https://github.com/lkuchenb) from the [Kohlbacher Lab](https://kohlbacherlab.org/).
 
 ## Contributions and Support
 

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 -

bin/epaa.py

@@ -1011,7 +1011,7 @@ def __main__():
         # NOTE this needs to be updated, if a newer version will be available via Fred2 and should be used in the future
         tool_version.append(('syfpeithi', '1.0'))
         # get for each selected method the corresponding tool version
-        methods = { method:version for tool, version in tool_version for method in selected_methods if tool.lower() in method.lower() }
+        methods = { method.lower() : version for tool, version in tool_version for method in selected_methods if tool.lower() in method.lower() }
 
     for method, version in methods.items():
         if version not in EpitopePredictorFactory.available_methods()[method]:
@@ -1038,7 +1038,7 @@ def __main__():
 
     # replace method names with method names with version
     # complete_df.replace({'method': methods}, inplace=True)
-    complete_df['method'] = complete_df['method'].apply(lambda x : x + '-' + methods[x] )
+    complete_df['method'] = complete_df['method'].apply(lambda x : x.lower() + '-' + methods[x.lower()] )
 
     # include wild type sequences to dataframe if specified
     if args.wild_type:
@@ -1149,4 +1149,4 @@ def __main__():
     logger.info("Finished predictions at " + str(datetime.now().strftime("%Y-%m-%d %H:%M:%S")))
 
 if __name__ == "__main__":
-    __main__()
+    __main__()

bin/scrape_software_versions.py

@@ -12,6 +12,10 @@
     'Fred2': ['v_fred2.txt', r"fred2 (\S+)"],
     'MHCFlurry': ['v_mhcflurry.txt', r"mhcflurry (\S+)"],
     'MHCnuggets': ['v_mhcnuggets.txt', r"mhcnuggets (\S+)"],
+    'NetMHC': ['v_netmhc.txt', r"netmhc (\S+)"],
+    'NetMHCpan': ['v_netmhcpan.txt', r"netmhcpan (\S+)"],
+    'NetMHCII': ['v_netmhcii.txt', r"netmhcii (\S+)"],
+    'NetMHCIIpan': ['v_netmhciipan.txt', r"netmhciipan (\S+)"],
 }
 
 results = OrderedDict()
@@ -23,6 +27,10 @@
 results['Fred2'] = '<span style="color:#999999;\">N/A</span>'
 results['MHCFlurry'] = '<span style="color:#999999;\">N/A</span>'
 results['MHCnuggets'] = '<span style="color:#999999;\">N/A</span>'
+results['NetMHC'] = '<span style="color:#999999;\">N/A</span>'
+results['NetMHCpan'] = '<span style="color:#999999;\">N/A</span>'
+results['NetMHCII'] = '<span style="color:#999999;\">N/A</span>'
+results['NetMHCIIpan'] = '<span style="color:#999999;\">N/A</span>'
 
 # Search each file using its regex
 for k, v in regexes.items():

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'
+}