set all extentions to lower case for simple extention detection

nf-core · May 28, 2024 · 586d473 · 586d473
1 parent 3caf8c7
commit 586d473
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/subworkflows/local/prepare_spectra.nf b/subworkflows/local/prepare_spectra.nf
@@ -23,7 +23,7 @@ workflow PREPARE_SPECTRA {
                     return [ meta, filename ]
                 mzml : meta.ext == 'mzml'
                     return [ meta.subMap('id', 'sample', 'condition', 'group_count', 'spectra'), filename ]
-                mzml_gz : meta.ext == 'mzML.gz'
+                mzml_gz : meta.ext == 'mzml.gz'
                     return [ meta.subMap('id', 'sample', 'condition', 'group_count', 'spectra'), filename ]
                 d : meta.ext == 'd'
                     return [ meta.subMap('id', 'sample', 'condition', 'group_count', 'spectra'), filename ]

diff --git a/subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf b/subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf
@@ -164,7 +164,7 @@ def validateInputSamplesheet(input) {
 def getCustomExtension(file) {
     def name = file.getName()
     if (name =~ /.*\.(d\.tar\.gz|d\.tar|d\.zip|mzML\.gz|raw|RAW|mzML|d)$/) {
-        return name.split("\\.").drop(1).join(".")
+        return name.split("\\.").drop(1).join(".").toLowerCase()
     } else {
         return file.getExtension().toLowerCase()
     }