From 89eee34df9a98a170af185cc4bd4f28b6816741a Mon Sep 17 00:00:00 2001
From: Chris Cheshire <chris.j.cheshire@gmail.com>
Date: Wed, 16 Dec 2020 11:04:46 +0000
Subject: [PATCH] seacr | Added callpeak skeletonmain.nf

---
 software/seacr/callpeak/functions.nf | 59 ++++++++++++++++++++++++++++
 software/seacr/callpeak/main.nf      |  0
 software/seacr/callpeak/meta.yml     |  0
 3 files changed, 59 insertions(+)
 create mode 100644 software/seacr/callpeak/functions.nf
 create mode 100644 software/seacr/callpeak/main.nf
 create mode 100644 software/seacr/callpeak/meta.yml

diff --git a/software/seacr/callpeak/functions.nf b/software/seacr/callpeak/functions.nf
new file mode 100644
index 00000000..b3ac3801
--- /dev/null
+++ b/software/seacr/callpeak/functions.nf
@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}
diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf
new file mode 100644
index 00000000..e69de29b
diff --git a/software/seacr/callpeak/meta.yml b/software/seacr/callpeak/meta.yml
new file mode 100644
index 00000000..e69de29b