add basic GitHub action testing

.github/workflows/push-stub-run.yml

@@ -0,0 +1,31 @@
+name: Nextflow Stub Run
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ '**' ]
+
+jobs:
+  stub-run:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        config: [
+          'test-diann.config',
+          'test-encyclopedia-narrow-gpf.config',
+          'test-encyclopedia-wide-only.config'
+        ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Run (${{ matrix.config }})
+      run: |
+        echo "Installing Nextflow:"
+        curl -s https://get.nextflow.io | bash
+        chmod +x nextflow
+        echo "Running Nextflow stub with config: ${{ matrix.config }}"
+        ./nextflow secrets set PANORAMA_API_KEY "PLACEHOLDER"
+        ./nextflow run . -stub-run -c test-resources/${{ matrix.config }}

resources/pipeline.config

@@ -1,114 +0,0 @@
-//
-// A sample pipeline.config for running the TEI-REX DIA Nextflow workflow.
-//
-// See https://nf-skyline-dia-ms.readthedocs.io/en/latest/workflow_options.html
-// for a complete description of all parameters.
-//
-// Send questions, comments, ideas, bug reports, etc, to:
-// Michael Riffle <[email protected]>
-//
-
-// params will need changed per workflow run
-params {
-
-    // the data to be processed.
-
-	// note: files and directories may specify a local file or a PanoramaWeb WebDAV directory/file
-	// Example local file:
-	//    spectral_library = '/path/to/file.dlib'
-	//
-	// Example PanoramaWeb WebDAV location:
-	//    spectral_library = 'https://panoramaweb.org/_webdav/DIRECTORY/RawFiles/file.dlib'
-
-	// the data to be quantified (e.g., wide window data)
-    quant_spectra_dir = '/path/to/wide_window_data'
-
-	// which files in this directory to use, default: all raw files
-	//quant_spectra_glob = '*.raw'
-
-	// Optional: the data to be used to generate a chromatogram library (elib)
-	// if missing the chromatogram library step will be skipped
-    chromatogram_library_spectra_dir = '/path/to/narrow_window_data'
-
-	// which files in this directory to use, default: all raw files
-	//chromatogram_library_spectra_glob = '*.raw'
-
-	// spectral library used for searching
-    spectral_library = '/path/to/file.dlib'
-
-	// the background FASTA file
-    fasta = '/path/to/file.fasta'
-
-	// options for msconvert
-    msconvert.do_demultiplex = true;          // whether or not to demultiplex with msconvert
-    msconvert.do_simasspectra = true;         // whether or not to do simAsSpectra with msconvert
-
-    // default parameters for Encyclopedia searches, can be overridden
-    encyclopedia.chromatogram.params    = '-enableAdvancedOptions -v2scoring'
-    encyclopedia.quant.params           = '-enableAdvancedOptions -v2scoring'
-
-    // whether or not to save the output from encyclopedia running on individual raw/mzML
-    // files (e.g. .dia or .features.txt files) to the results directory
-    // the generated chromatogram library (elib) will always be saved, regardless of this setting
-    encyclopedia.save_output            = false
-
-	// Optional: the skyline template file used to create final skyline document
-	// if missing, commented out, or set to null, a default document will be used
-    //skyline_template_file     = './template.sky.zip'
-
-    // replicate metadata
-    // Can be in csv or tsv format.
-    // Each row in the file represents a replicate.
-    // The first column should have the heading 'Replicate' and the values in the column should
-    // match the raw file base names. There should be an additional column for each metadata
-    // variable. The column header is the name of the variable and the values in the column are
-    // the annotations corresponding to each replicate.
-    replicate_metadata = null
-
-    // Skip QC report generation
-    qc_report.skip = false
-
-    // List of protein names to plot retention times for
-    qc_report.standard_proteins = null
-
-    // List of metadata variables to color PCA plots by
-    qc_report.color_vars = null
-
-    // Export matrices of normalized precursor and protein quantities?
-    qc_report.export_tables = false
-
-    // receive email when done at this address
-    // note: the email config at the end of this file must be set up for this to work
-    // if commented out (default), no attempt to send email will be made
-    //email = '[email protected]'
-}
-
-// if running jobs locally change these to match system capabilities
-profiles {
-
-    // "standard" is the profile used when the steps of the workflow are run
-    // locally on your computer. These parameters should be changed to match
-    // your system resources (that you are willing to devote to running
-    // workflow jobs).
-    standard {
-        params.max_memory = '8.GB'
-        params.max_cpus = 4
-        params.max_time = '240.h'
-
-        params.mzml_cache_directory = '/data/mass_spec/nextflow/nf-skyline-dia-ms/mzml_cache'
-        params.panorama_cache_directory = '/data/mass_spec/nextflow/panorama/raw_cache'
-    }
-}
-
-// advanced config: change settings to match your email provider to send emails
-mail {
-    from = '[email protected]'
-    smtp.host = 'smtp.host.com'
-    smtp.port = 587
-    smtp.user = 'smpt_user'
-    smtp.password = 'smtp_password'
-    smtp.auth = true
-    smtp.starttls.enable = true
-    smtp.starttls.required = false
-    mail.smtp.ssl.protocols = 'TLSv1.2'
-}

test-resources/narrow-window/test_wide1.raw

@@ -0,0 +1 @@
+dummy raw file

test-resources/narrow-window/test_wide2.raw

@@ -0,0 +1 @@
+dummy raw file

test-resources/test-diann.config

@@ -0,0 +1,117 @@
+//
+// A sample pipeline.config for running the TEI-REX DIA Nextflow workflow.
+//
+// See https://nf-skyline-dia-ms.readthedocs.io/en/latest/workflow_options.html
+// for a complete description of all parameters.
+//
+// Send questions, comments, ideas, bug reports, etc, to:
+// Michael Riffle <[email protected]>
+//
+
+// params will need changed per workflow run
+params {
+
+    // the data to be processed.
+
+	// note: files and directories may specify a local file or a PanoramaWeb WebDAV directory/file
+	// Example local file:
+	//    spectral_library = '/path/to/file.dlib'
+	//
+	// Example PanoramaWeb WebDAV location:
+	//    spectral_library = 'https://panoramaweb.org/_webdav/DIRECTORY/RawFiles/file.dlib'
+
+    // the search engine to use
+    search_engine = 'diann'
+
+	// the data to be quantified (e.g., wide window data)
+    quant_spectra_dir = 'test-resources/wide-window'
+
+	// which files in this directory to use, default: all raw files
+	quant_spectra_glob = '*.raw'
+
+	// Optional: the data to be used to generate a chromatogram library (elib)
+	// if missing the chromatogram library step will be skipped
+    //chromatogram_library_spectra_dir = '/path/to/narrow_window_data'
+
+	// which files in this directory to use, default: all raw files
+	//chromatogram_library_spectra_glob = '*.raw'
+
+	// spectral library used for searching
+    //spectral_library = '/path/to/file.dlib'
+
+	// the background FASTA file
+    fasta = 'test-resources/test.fasta'
+
+	// options for msconvert
+    msconvert.do_demultiplex = true;          // whether or not to demultiplex with msconvert
+    msconvert.do_simasspectra = true;         // whether or not to do simAsSpectra with msconvert
+
+    // default parameters for Encyclopedia searches, can be overridden
+    encyclopedia.chromatogram.params    = '-enableAdvancedOptions -v2scoring'
+    encyclopedia.quant.params           = '-enableAdvancedOptions -v2scoring'
+
+    // whether or not to save the output from encyclopedia running on individual raw/mzML
+    // files (e.g. .dia or .features.txt files) to the results directory
+    // the generated chromatogram library (elib) will always be saved, regardless of this setting
+    encyclopedia.save_output            = false
+
+	// Optional: the skyline template file used to create final skyline document
+	// if missing, commented out, or set to null, a default document will be used
+    //skyline_template_file     = './template.sky.zip'
+
+    // replicate metadata
+    // Can be in csv or tsv format.
+    // Each row in the file represents a replicate.
+    // The first column should have the heading 'Replicate' and the values in the column should
+    // match the raw file base names. There should be an additional column for each metadata
+    // variable. The column header is the name of the variable and the values in the column are
+    // the annotations corresponding to each replicate.
+    replicate_metadata = null
+
+    // Skip QC report generation
+    qc_report.skip = false
+
+    // List of protein names to plot retention times for
+    qc_report.standard_proteins = null
+
+    // List of metadata variables to color PCA plots by
+    qc_report.color_vars = null
+
+    // Export matrices of normalized precursor and protein quantities?
+    qc_report.export_tables = false
+
+    // receive email when done at this address
+    // note: the email config at the end of this file must be set up for this to work
+    // if commented out (default), no attempt to send email will be made
+    //email = '[email protected]'
+}
+
+// if running jobs locally change these to match system capabilities
+profiles {
+
+    // "standard" is the profile used when the steps of the workflow are run
+    // locally on your computer. These parameters should be changed to match
+    // your system resources (that you are willing to devote to running
+    // workflow jobs).
+    standard {
+        params.max_memory = '8.GB'
+        params.max_cpus = 4
+        params.max_time = '1.h'
+
+        params.mzml_cache_directory = './mzml_cache'
+        params.panorama_cache_directory = './raw_cache'
+    }
+}
+
+// advanced config: change settings to match your email provider to send emails
+mail {
+    from = '[email protected]'
+    smtp.host = 'smtp.host.com'
+    smtp.port = 587
+    smtp.user = 'smpt_user'
+    smtp.password = 'smtp_password'
+    smtp.auth = true
+    smtp.starttls.enable = true
+    smtp.starttls.required = false
+    mail.smtp.ssl.protocols = 'TLSv1.2'
+}

test-resources/test-encyclopedia-narrow-gpf.config

@@ -0,0 +1,117 @@
+//
+// A sample pipeline.config for running the TEI-REX DIA Nextflow workflow.
+//
+// See https://nf-skyline-dia-ms.readthedocs.io/en/latest/workflow_options.html
+// for a complete description of all parameters.
+//
+// Send questions, comments, ideas, bug reports, etc, to:
+// Michael Riffle <[email protected]>
+//
+
+// params will need changed per workflow run
+params {
+
+    // the data to be processed.
+
+	// note: files and directories may specify a local file or a PanoramaWeb WebDAV directory/file
+	// Example local file:
+	//    spectral_library = '/path/to/file.dlib'
+	//
+	// Example PanoramaWeb WebDAV location:
+	//    spectral_library = 'https://panoramaweb.org/_webdav/DIRECTORY/RawFiles/file.dlib'
+
+    // the search engine to use
+    search_engine = 'encyclopedia'
+
+	// the data to be quantified (e.g., wide window data)
+    quant_spectra_dir = 'test-resources/wide-window'
+
+	// which files in this directory to use, default: all raw files
+	quant_spectra_glob = '*.raw'
+
+	// Optional: the data to be used to generate a chromatogram library (elib)
+	// if missing the chromatogram library step will be skipped
+    chromatogram_library_spectra_dir = 'test-resources/narrow-window'
+
+	// which files in this directory to use, default: all raw files
+	chromatogram_library_spectra_glob = '*.raw'
+
+	// spectral library used for searching
+    spectral_library = 'test-resources/test.dlib'
+
+	// the background FASTA file
+    fasta = 'test-resources/test.fasta'
+
+	// options for msconvert
+    msconvert.do_demultiplex = true;          // whether or not to demultiplex with msconvert
+    msconvert.do_simasspectra = true;         // whether or not to do simAsSpectra with msconvert
+
+    // default parameters for Encyclopedia searches, can be overridden
+    encyclopedia.chromatogram.params    = '-enableAdvancedOptions -v2scoring'
+    encyclopedia.quant.params           = '-enableAdvancedOptions -v2scoring'
+
+    // whether or not to save the output from encyclopedia running on individual raw/mzML
+    // files (e.g. .dia or .features.txt files) to the results directory
+    // the generated chromatogram library (elib) will always be saved, regardless of this setting
+    encyclopedia.save_output            = false
+
+	// Optional: the skyline template file used to create final skyline document
+	// if missing, commented out, or set to null, a default document will be used
+    //skyline_template_file     = './template.sky.zip'
+
+    // replicate metadata
+    // Can be in csv or tsv format.
+    // Each row in the file represents a replicate.
+    // The first column should have the heading 'Replicate' and the values in the column should
+    // match the raw file base names. There should be an additional column for each metadata
+    // variable. The column header is the name of the variable and the values in the column are
+    // the annotations corresponding to each replicate.
+    replicate_metadata = null
+
+    // Skip QC report generation
+    qc_report.skip = false
+
+    // List of protein names to plot retention times for
+    qc_report.standard_proteins = null
+
+    // List of metadata variables to color PCA plots by
+    qc_report.color_vars = null
+
+    // Export matrices of normalized precursor and protein quantities?
+    qc_report.export_tables = false
+
+    // receive email when done at this address
+    // note: the email config at the end of this file must be set up for this to work
+    // if commented out (default), no attempt to send email will be made
+    //email = '[email protected]'
+}
+
+// if running jobs locally change these to match system capabilities
+profiles {
+
+    // "standard" is the profile used when the steps of the workflow are run
+    // locally on your computer. These parameters should be changed to match
+    // your system resources (that you are willing to devote to running
+    // workflow jobs).
+    standard {
+        params.max_memory = '8.GB'
+        params.max_cpus = 4
+        params.max_time = '1.h'
+
+        params.mzml_cache_directory = './mzml_cache'
+        params.panorama_cache_directory = './raw_cache'
+    }
+}
+
+// advanced config: change settings to match your email provider to send emails
+mail {
+    from = '[email protected]'
+    smtp.host = 'smtp.host.com'
+    smtp.port = 587
+    smtp.user = 'smpt_user'
+    smtp.password = 'smtp_password'
+    smtp.auth = true
+    smtp.starttls.enable = true
+    smtp.starttls.required = false
+    mail.smtp.ssl.protocols = 'TLSv1.2'
+}