fix blank example pipeline.config file

resources/pipeline.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 <mriffle@uw.edu>
+//
+
+// 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'
+
+    // the search engine to use, must be one of 'diann' or 'encyclopedia'
+    search_engine = 'encyclopedia'
+
+	// 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@host.com'
+}
+
+// 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 = 'address@host.com'
+    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'
+}