added plex6tmt from MSnbase

assets/tmt6plex_default_correction.matrix

@@ -1,7 +1,9 @@
+# comment: tmt6plex from MSnbase
+# comment: https://github.com/lgatto/MSnbase/blob/master/inst/extdata/TMT6plexPurityCorrections.csv
 channel/<-2Da>/<-1Da>/<+1Da>/<+2Da>
-126/0.0/0.0/0.0/0.0
-127/0.0/0.0/0.0/0.0
-128/0.0/0.0/0.0/0.0
-129/0.0/0.0/0.0/0.0
-130/0.0/0.0/0.0/0.0
-131/0.0/0.0/0.0/0.0
+126/0.0/0.0/6.1/0.0
+127/0.0/0.5/6.7/0.0
+128/0.0/1.1/4.2/0.0
+129/0.0/1.7/4.1/0.0
+130/0.0/1.6/2.1/0.0
+131/0.2/3.2/2.8/0.0

modules/local/openms/isobaricanalyzer/main.nf

@@ -35,7 +35,10 @@ process ISOBARICANALYZER {
         }
 
         // Read the matrix file and format it into the command-line format
-        def matrix_lines = new File(params.plex_corr_matrix_file).readLines().drop(1).collect { line ->
+        def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
+        .findAll { !it.startsWith('#') && it.trim() } // Skip lines starting with '#' and empty lines
+        .drop(1) // Assuming the first non-comment line is a header
+        .collect { line ->
             def values = line.split('/')
             return "${values[1]}/${values[2]}/${values[3]}/${values[4]}"
         }