Merge branch 'dev' into dev

CHANGELOG.md

@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - DeepLC retention time prediction
 - MS2PIP peak intensity prediction
 - Added OpenMS FileFilter to clean mzml after parsing to remove artifacts like empty spectra or precursors with charge 0
+- Made file extension check case insensitive
+- Added option to provide a default comet parameters file
 - Optimize resource allocations
 
 ### `Fixed`

bin/check_samplesheet.py

@@ -25,7 +25,7 @@ class RowChecker:
 
     """
 
-    VALID_FORMATS = (".raw", ".mzML", ".d")
+    VALID_FORMATS = (".raw", ".mzml", ".d")
 
     def __init__(
         self,
@@ -93,7 +93,7 @@ def _validate_filename(self, row):
 
     def _validate_ms_format(self, filename):
         """Assert that a given filename has one of the expected MS extensions."""
-        assert any(filename.endswith(extension) for extension in self.VALID_FORMATS), (
+        assert any(filename.lower().endswith(extension) for extension in self.VALID_FORMATS), (
             f"The file has an unrecognized extension: {filename}\n"
             f"It should be one of: {', '.join(self.VALID_FORMATS)}"
         )

modules/local/openms_cometadapter.nf

@@ -23,6 +23,7 @@ process OPENMS_COMETADAPTER {
         def args             = task.ext.args  ?: ''
 
         def mods             = params.fixed_mods != " " ? "-fixed_modifications ${params.fixed_mods.tokenize(',').collect { "'${it}'"}.join(" ")}" : "-fixed_modifications"
+        def params_file      = params.default_params_file_comet != " " ? "-default_params_file ${params.default_params_file_comet}" : ""
         def xions            = params.use_x_ions ? "-use_X_ions true" : ""
         def zions            = params.use_z_ions ? "-use_Z_ions true" : ""
         def aions            = params.use_a_ions ? "-use_A_ions true" : ""
@@ -36,6 +37,7 @@ process OPENMS_COMETADAPTER {
             -database $fasta \\
             -threads $task.cpus \\
             -pin_out ${prefix}.tsv \\
+            $params_file \\
             $args \\
             $mods \\
             $xions \\

nextflow.config

@@ -36,6 +36,7 @@ params {
     fragment_bin_offset             = 0.0
     fragment_mass_tolerance         = 0.01
     instrument                      = 'high_res'
+    default_params_file_comet       = ' '
     klammer                         = false
     max_rt_alignment_shift          = 300
     number_mods                     = 3

nextflow_schema.json

@@ -337,6 +337,11 @@
                     "type": "string",
                     "fa_icon": "fas fa-train-track",
                     "description": "MS2pip model name defined (https://github.com/compomics/ms2pip#specialized-prediction-models)"
+                },
+                "default_params_file_comet": {
+                    "type": "string",
+                    "fa_icon": "fas fa-file-code",
+                    "description": "Default Comet params file. All parameters of this take precedence."
                 }
             }
         },