Add test profi

.github/workflows/ci.yml

@@ -39,25 +39,41 @@ jobs:
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --spectrum_batch_size 5000 --outdir ./results
 
-  test_additional_params:
+  profiles:
     name: Run pipeline with additional params
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}"
     runs-on: ubuntu-latest
+    env:
+      NXF_VER: ${{ matrix.nxf_ver }}
+      NXF_ANSI_LOG: false
     strategy:
       matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
+        include:
+          - NXF_VER:
+              - "23.04.0"
+              - "latest-everything"
+        tests:
+          [
+            "test_deeplc",
+            "test_ms2pip",
+            "test_quant",
+            "test_ionannotator",
+            "test_full"
+          ]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
-        with:
+        env:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with additional params
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --spectrum_batch_size 2000 --use_deeplc --use_ms2pip --ms2pip_model_name 'CID' --annotate_ions --outdir ./results
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Run pipeline with profile ${{ matrix.tests }}
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --outdir ./results

conf/test_deeplc.config

@@ -0,0 +1,33 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests with DeepLC
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mhcquant -profile test_deeplc,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test DeepLC profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function with DeepLC'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/UP000005640_9606.fasta'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/HepG2_sample_sheet.tsv'
+
+    // Don't do quantification since this step needs a larger test dataset (-> test quantification using test_full)
+    skip_quantification     = true
+    spectrum_batch_size     = 5000
+    use_deeplc              = true
+    deeplc_add_abs_rt_error = true
+    deeplc_add_sqr_rt_error = true
+    deeplc_add_log_rt_error = true
+}

conf/test_full.config

@@ -14,10 +14,15 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    predict_class_1 = true
-
     // Input data
     fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/UP000005640_9606.fasta'
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/sample_sheet_full.tsv'
     allele_sheet = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/allele_sheet_full.tsv'
+
+    predict_class_1   = true
+    predict_class_2   = true
+    use_deeplc        = true
+    use_ms2pip        = true
+    ms2pip_model_name = 'CID'
+    annotate_ions     = true
 }

conf/test_ionannotator.config

@@ -0,0 +1,30 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running ion annotator tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mhcquant -profile test_ionannotator,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test ion annotator profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function with ion annotator'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/UP000005640_9606.fasta'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/HepG2_sample_sheet.tsv'
+
+    // Don't do quantification since this step needs a larger test dataset (-> test quantification using test_full)
+    skip_quantification = true
+    spectrum_batch_size = 5000
+    annotate_ions       = true
+}

conf/test_ms2pip.config

@@ -0,0 +1,31 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests with MS2PIP
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mhcquant -profile test_ms2pip,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test MS2PIP profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function with MS2PIP'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/UP000005640_9606.fasta'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/HepG2_sample_sheet.tsv'
+
+    // Don't do quantification since this step needs a larger test dataset (-> test quantification using test_full)
+    skip_quantification = true
+    spectrum_batch_size = 5000
+    use_ms2pip          = true
+    ms2pip_model_name   = 'Immuno-HCD'
+}

conf/test_quant.config

@@ -0,0 +1,22 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running quantification tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a full size pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/mhcquant -profile test_quant,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Quantification test profile'
+    config_profile_description = 'Quantification test dataset to check pipeline function'
+
+    // Input data
+    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/UP000005640_9606.fasta'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/sample_sheet_full.tsv'
+
+    spectrum_batch_size = 2000
+}