Add msconvert-only github action tests.

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

@@ -15,7 +15,9 @@ jobs:
           'test-diann.config',
           'test-encyclopedia-narrow-gpf.config',
           'test-encyclopedia-wide-only.config',
-          'test-diann-pdc.config'
+          'test-diann-pdc.config',
+          'test-msconvert-only-pdc.config',
+          'test-msconvert-only-local.config'
         ]
 
     steps:

test-resources/test-msconvert-only-local.config

@@ -0,0 +1,39 @@
+//
+// 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 {
+
+    chromatogram_library_spectra_dir = 'test-resources/narrow-window'
+    quant_spectra_dir = 'test-resources/wide-window'
+
+	// 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
+
+    msconvert_only = true
+}
+
+// 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'
+    }
+}

test-resources/test-msconvert-only-pdc.config

@@ -0,0 +1,39 @@
+//
+// 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 {
+
+    pdc.study_id = 'PDC000504'
+    pdc.n_raw_files = 2
+
+	// options for msconvert
+    msconvert.do_demultiplex = false;          // whether or not to demultiplex with msconvert
+    msconvert.do_simasspectra = true;         // whether or not to do simAsSpectra with msconvert
+
+    msconvert_only = true
+}
+
+// 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'
+    }
+}