--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/centrifuge.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,54 @@
+// Help text for centrifuge within CPIPES.
+
+def centrifugeHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'centrifuge_x': [
+            clihelp: "Absolute path to centrifuge database. Default: ${params.centrifuge_x}",
+            cliflag: '-x',
+            clivalue: null
+        ],
+        'centrifuge_save_unaligned': [
+            clihelp: 'Save SINGLE-END reads that did not align. For PAIRED-END' +
+                " reads, save read pairs that did not align concordantly. Default: ${params.centrifuge_save_unaligned}",
+            cliflag: null, // Handled in modules logic.
+            clivalue: null
+        ],
+        'centrifuge_save_aligned': [
+            clihelp: 'Save SINGLE-END reads that aligned. For PAIRED-END' +
+                " reads, save read pairs that aligned concordantly. Default: ${params.centrifuge_save_aligned}",
+            cliflag: null, // Handled in modules logic.
+            clivalue: null
+        ],
+        'centrifuge_out_fmt_sam': [
+            clihelp: "Centrifuge output should be in SAM. Default: ${params.centrifuge_save_aligned}",
+            cliflag: null, // Handled in modules logic.
+            clivalue: null
+        ],
+        'centrifuge_extract_bug': [
+            clihelp: "Extract this bug from centrifuge results." +
+                " Default: ${params.centrifuge_extract_bug}",
+            cliflag: null, // Handled in modules logic.
+            clivalue: null,
+        ],
+        'centrifuge_ignore_quals': [
+            clihelp: 'Treat all quality values as 30 on Phred scale. ' +
+                "Default: ${params.centrifuge_ignore_quals}",
+            cliflag: '--ignore-quals',
+            clivalue: (params.centrifuge_ignore_quals ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
+