From 994c0694e912fe23b156bfd62c820c781a70f80b Mon Sep 17 00:00:00 2001
From: veitveit <veitveit@gmail.com>
Date: Mon, 3 Jan 2022 11:27:27 +0100
Subject: [PATCH] removed file

---
 modules/maxquant/lfq/functions.nf | 68 -------------------------------
 modules/maxquant/lfq/t            |  2 -
 2 files changed, 70 deletions(-)
 delete mode 100644 modules/maxquant/lfq/functions.nf
 delete mode 100644 modules/maxquant/lfq/t

diff --git a/modules/maxquant/lfq/functions.nf b/modules/maxquant/lfq/functions.nf
deleted file mode 100644
index da9da093..00000000
--- a/modules/maxquant/lfq/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/maxquant/lfq/t b/modules/maxquant/lfq/t
deleted file mode 100644
index c3efa92e..00000000
--- a/modules/maxquant/lfq/t
+++ /dev/null
@@ -1,2 +0,0 @@
-[?1h=MaxQuantCmd 1.6.10.43
-[?1l>
\ No newline at end of file