From 586d4739c258975ded4d63fd0a8c4f4c5d5a6bc3 Mon Sep 17 00:00:00 2001 From: Jonas Scheid Date: Tue, 28 May 2024 20:48:28 +0000 Subject: [PATCH] set all extentions to lower case for simple extention detection --- subworkflows/local/prepare_spectra.nf | 2 +- subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/prepare_spectra.nf b/subworkflows/local/prepare_spectra.nf index 0e7bd14f..9acacd6d 100644 --- 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 index dd5801b6..cc178b95 100644 --- 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() }