--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/bbmerge.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,186 @@
+// Help text for bbmerge within CPIPES.
+
+def bbmergeHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'bbmerge_run': [
+            clihelp: 'Run BBMerge tool. Default: ' +
+                (params.bbmerge_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'bbmerge_reads': [
+            clihelp: 'Quit after this many read pairs (-1 means all) ' +
+                "Default: ${params.bbmerge_reads}",
+            cliflag: 'reads=',
+            clivalue: (params.bbmerge_reads ?: '')
+        ],
+        'bbmerge_adapters': [
+            clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
+                "FASTA format. Default: ${params.bbmerge_adapters}",
+            cliflag: 'adapters=',
+            clivalue: (params.bbmerge_adapters ?: '')
+        ],
+        'bbmerge_ziplevel': [
+            clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
+                "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
+            cliflag: 'ziplevel=',
+            clivalue: (params.bbmerge_ziplevel ?: '')
+        ],
+        'bbmerge_ordered': [
+            clihelp: 'Output reads in the same order as input. ' +
+                "Default: ${params.bbmerge_ordered}",
+            cliflag: 'ordered=',
+            clivalue: (params.bbmerge_ordered ?: '')
+        ],
+        'bbmerge_qtrim': [
+            clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
+                'Trims BEFORE merging. Values: t (trim both ends), ' + 
+                'f (neither end), r (right end only), l (left end only). ' +
+                "Default: ${params.bbmerge_qtrim}",
+            cliflag: 'qtrim=',
+            clivalue: (params.bbmerge_qtrim ?: '')
+        ],
+        'bbmerge_qtrim2': [
+            clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
+                'only if merging is unsuccesful. then retry merging. ' +
+                "Default: ${params.bbmerge_qtrim2}",
+            cliflag: 'qtrim2=',
+            clivalue: (params.bbmerge_qtrim2 ?: '')
+        ],
+        'bbmerge_trimq': [
+            clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
+                "to try multiple values. Default: ${params.bbmerge_trimq}",
+            cliflag: 'trimq=',
+            clivalue: (params.bbmerge_trimq ?: '')
+        ],
+        'bbmerge_minlength': [
+            clihelp: '(ml) Reads shorter than this after trimming, but before ' +
+                'merging, will be discarded. Pairs will be discarded only' +
+                "if both are shorter. Default: ${params.bbmerge_minlength}",
+            cliflag: 'minlength=',
+            clivalue: (params.bbmerge_minlength ?: '')
+        ],
+        'bbmerge_tbo': [
+            clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
+                "most (3') non-overlaping portion instead of joining " +
+                "Default: ${params.bbmerge_tbo}",
+            cliflag: 'tbo=',
+            clivalue: (params.bbmerge_tbo ?: '')
+        ],
+        'bbmerge_minavgquality': [
+            clihelp: '(maq). Reads with average quality below this after trimming will ' +
+                "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
+            cliflag: 'minavgquality=',
+            clivalue: (params.bbmerge_minavgquality ?: '')
+        ],
+        'bbmerge_trimpolya': [
+            clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
+                'outadapter.  This also trims poly-A followed by poly-G, which ' +
+                "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
+            cliflag: 'trimpolya=',
+            clivalue: (params.bbmerge_trimpolya ?: '')
+        ],
+        'bbmerge_pfilter': [
+            clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
+                'disable the filter; 1 will allow only perfect overlaps. ' +
+                "Default: ${params.bbmerge_pfilter}",
+            cliflag: 'pfilter=',
+            clivalue: (params.bbmerge_pfilter ?: '')
+        ],
+        'bbmerge_ouq': [
+            clihelp: 'Calculate best overlap using quality values. ' +
+                "Default: ${params.bbmerge_ouq}",
+            cliflag: 'ouq',
+            clivalue: (params.bbmerge_ouq ?: '')
+        ],
+        'bbmerge_owq': [
+            clihelp: 'Calculate best overlap without using quality values. ' +
+                "Default: ${params.bbmerge_owq}",
+            cliflag: 'owq=',
+            clivalue: (params.bbmerge_owq ?: '')
+        ],
+        'bbmerge_strict': [
+            clihelp: 'Decrease false positive rate and merging rate. ' +
+                "Default: ${params.bbmerge_strict}",
+            cliflag: 'strict=',
+            clivalue: (params.bbmerge_strict ?: '')
+        ],
+        'bbmerge_verystrict': [
+            clihelp: 'Greatly decrease false positive rate and merging rate. ' +
+                "Default: ${params.bbmerge_verystrict}",
+            cliflag: 'verystrict=',
+            clivalue: (params.bbmerge_verystrict ?: '')
+        ],
+        'bbmerge_ultrastrict': [
+            clihelp: 'Decrease false positive rate and merging rate even more. ' +
+                "Default: ${params.bbmerge_ultrastrict}",
+            cliflag: 'ultrastrict=',
+            clivalue: (params.bbmerge_ultrastrict ?: '')
+        ],
+        'bbmerge_maxstrict': [
+            clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
+                "Default: ${params.bbmerge_maxstrict}",
+            cliflag: 'maxstrict=',
+            clivalue: (params.bbmerge_maxstrict ?: '')
+        ],
+        'bbmerge_loose': [
+            clihelp: 'Increase false positive rate and merging rate. ' +
+                "Default: ${params.bbmerge_loose}",
+            cliflag: 'loose=',
+            clivalue: (params.bbmerge_loose ?: '')
+        ],
+        'bbmerge_veryloose': [
+            clihelp: 'Greatly increase false positive rate and merging rate. ' +
+                "Default: ${params.bbmerge_veryloose}",
+            cliflag: 'veryloose=',
+            clivalue: (params.bbmerge_veryloose ?: '')
+        ],
+        'bbmerge_ultraloose': [
+            clihelp: 'Increase false positive rate and merging rate even more. ' +
+                "Default: ${params.bbmerge_ultraloose}",
+            cliflag: 'ultraloose=',
+            clivalue: (params.bbmerge_ultraloose ?: '')
+        ],
+        'bbmerge_maxloose': [
+            clihelp: 'Maximally increase false positive rate and merging rate. ' +
+                "Default: ${params.bbmerge_maxloose}",
+            cliflag: 'maxloose=',
+            clivalue: (params.bbmerge_maxloose ?: '')
+        ],
+        'bbmerge_fast': [
+            clihelp: 'Fastest possible preset. ' +
+                "Default: ${params.bbmerge_fast}",
+            cliflag: 'fast=',
+            clivalue: (params.bbmerge_fast ?: '')
+        ],
+        'bbmerge_k': [
+            clihelp: 'Kmer length.  31 (or less) is fastest and uses the least ' +
+                'memory, but higher values may be more accurate. ' +
+                '60 tends to work well for 150bp reads. ' +
+                "Default: ${params.bbmerge_k}",
+            cliflag: 'k=',
+            clivalue: (params.bbmerge_k ?: '')
+        ],
+        'bbmerge_prealloc': [
+            clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
+                'Faster and more memory-efficient for large datasets. ' +
+                'A float fraction (0-1) may be specified, default 1. ' +
+                "Default: ${params.bbmerge_prealloc}",
+            cliflag: 'prealloc=',
+            clivalue: (params.bbmerge_prealloc ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file