--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/lib/help/filtlong.nf	Thu May 28 20:41:10 2026 +0000
@@ -0,0 +1,115 @@
+// Help text for filtlong within CPIPES.
+
+def filtlongHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'filtlong_run': [
+            clihelp: 'Run filtlong read trimming tool. Default: ' +
+                (params.filtlong_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'filtlong_keep_perc': [
+            clihelp: 'Keep only this percentage of best reads. ' +
+                "Default: ${params.filtlong_keep_perc}",
+            cliflag: '--keep_percent',
+            clivalue: (params.filtlong_keep_perc ?: '')
+        ],
+        'filtlong_target_bases': [
+            clihelp: 'Keep only the best bases up to this many total bases. ' +
+                "Default: ${params.filtlong_target_bases}",
+            cliflag: '--target_bases',
+            clivalue: (params.filtlong_target_bases ?: '')
+        ],
+        'filtlong_min_length': [
+            clihelp: 'Minimum length threshold. ' +
+                "Default: ${params.filtlong_min_length}",
+            cliflag: '--min_length',
+            clivalue: (params.filtlong_min_length ?: '')
+        ],
+        'filtlong_max_length': [
+            clihelp: 'Maximum length threshold. ' +
+                "Default: ${params.filtlong_max_length}",
+            cliflag: '--max_length',
+            clivalue: (params.filtlong_max_length ?: '')
+        ],
+        'filtlong_min_mean_q': [
+            clihelp: 'Minimum mean quality threshold. ' +
+                "Default: ${params.filtlong_min_mean_q}",
+            cliflag: '--min_mean_q',
+            clivalue: (params.filtlong_min_mean_q ?: '')
+        ],
+        'filtlong_min_window_q': [
+            clihelp: 'Minimum window quality threshold. ' +
+                "Default: ${params.filtlong_min_window_q}",
+            cliflag: '--min_window_q',
+            clivalue: (params.filtlong_min_window_q ?: '')
+        ],
+        'filtlong_a': [
+            clihelp: "External reference assembly in FASTA format. " +
+                "Default: ${params.filtlong_a}",
+            cliflag: '-a',
+            clivalue: (params.filtlong_a ?: '')
+        ],
+        'filtlong_1': [
+            clihelp: 'External reference Illumina reads in FASTQ format (R1). ' +
+                "Default: ${params.filtlong_1}",
+            cliflag: '-1',
+            clivalue: (params.filtlong_1 ?: '')
+        ],
+        'filtlong_2': [
+            clihelp: 'External reference Illumina reads in FASTQ format (R2). ' +
+                "Default: ${params.filtlong_2}",
+            cliflag: '--2',
+            clivalue: (params.filtlong_2 ?: '')
+        ],
+        'filtlong_len_weight': [
+            clihelp: 'Weight given to the length score. ' +
+                "Default: ${params.filtlong_len_weight}",
+            cliflag: '--length_weight',
+            clivalue: (params.filtlong_len_weight ?: '')
+        ],
+        'filtlong_mean_q_weight': [
+            clihelp: 'Weight given to the mean quality score. ' +
+                "Default: ${params.filtlong_mean_q_weight}",
+            cliflag: '--mean_q_weight',
+            clivalue: (params.filtlong_mean_q_weight ?: '')
+        ],
+        'filtlong_window_q_weight': [
+            clihelp: 'Weight given to the window quality score. ' +
+                "Default: ${params.filtlong_window_q_weight}",
+            cliflag: '--window_q_weight',
+            clivalue: (params.filtlong_window_q_weight ?: '')
+        ],
+        'filtlong_trim': [
+            clihelp: 'Trim non k-mer matching bases from start/end of the reads. ' +
+                "Default: ${params.filtlong_trim}",
+            cliflag: '--trim',
+            clivalue: (params.filtlong_trim ? ' ' : '')
+        ],
+        'filtlong_split': [
+            clihelp: 'Split reads at this many (or more) consecutive non k-mer matching bases. ' +
+                "Default: ${params.filtlong_split}",
+            cliflag: '--split',
+            clivalue: (params.filtlong_split ? ' ' : '')
+        ],
+        'filtlong_window_size': [
+            clihelp: 'Size of sliding window used when measuring window quality. ' +
+                "Default: ${params.filtlong_window_size}",
+            cliflag: '--window_size',
+            clivalue: (params.filtlong_window_size ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file