--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.6.1/lib/help/flye.nf	Tue Sep 05 11:51:40 2023 -0400
@@ -0,0 +1,82 @@
+// Help text for flye within CPIPES.
+
+def flyeHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'flye_pacbio_raw': [
+            clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' +
+                "Default: ${params.flye_pacbio_raw}",
+            cliflag: '--pacbio-raw',
+            clivalue: (params.flye_pacbio_raw ? ' ' : '')
+        ], 
+        'flye_pacbio_corr': [
+            clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' +
+                "with other methods (<3% error). Default: ${params.flye_pacbio_corr}",
+            cliflag: '--pacbio-corr',
+            clivalue: (params.flye_pacbio_corr ? ' ' : '')
+        ],
+        'flye_pacbio_hifi': [
+            clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' +
+                "Default: ${params.flye_pacbio_hifi}",
+            cliflag: '--pacbio-hifi',
+            clivalue: (params.flye_pacbio_hifi ? ' ' : '')
+        ],
+        'flye_nano_raw': [
+            clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' +
+                "Default: ${params.flye_nano_raw}",
+            cliflag: '--nano-raw',
+            clivalue: (params.flye_nano_raw ? ' ' : '')
+        ],
+        'flye_nano_corr': [
+            clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' +
+                "methods (<3% error). Default: ${params.flye_nano_corr}",
+            cliflag: '--nano-corr',
+            clivalue: (params.flye_nano_corr ? ' ' : '')
+        ],
+        'flye_nano_hq': [
+            clihelp: 'Input FASTQ reads are ONT high-quality reads: ' +
+                "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}",
+            cliflag: '--nano-hq',
+            clivalue: (params.flye_nano_hq ? ' ' : '')
+        ],
+        'flye_genome_size': [
+            clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' +
+                "Default: ${params.flye_genome_size}",
+            cliflag: '--genome-size',
+            clivalue: (params.flye_genome_size ?: '')
+        ],
+        'flye_polish_iter': [
+            clihelp: 'Number of genome polishing iterations. ' +
+                "Default: ${params.flye_polish_iter}",
+            cliflag: '--iterations',
+            clivalue: (params.flye_polish_iter ?: '')
+        ],
+        'flye_meta': [
+            clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}",
+            cliflag: '--meta',
+            clivalue: (params.flye_meta ? ' ' : '')
+        ],
+        'flye_min_overlap': [
+            clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}",
+            cliflag: '--min-overlap',
+            clivalue: (params.flye_min_overlap ?: '')
+        ],
+        'flye_scaffold': [
+            clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}",
+            cliflag: '--scaffold',
+            clivalue: (params.flye_scaffold ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file