--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/salmonidx.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,91 @@
+// Help text for salmon index within CPIPES.
+
+def salmonidxHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'salmonidx_run': [
+            clihelp: 'Run `salmon index` tool. Default: ' +
+                (params.salmonidx_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'salmonidx_k': [
+            clihelp: 'The size of k-mers that should be used for the ' +
+                " quasi index. Default: ${params.salmonidx_k}",
+            cliflag: '-k',
+            clivalue: (params.salmonidx_k ?: '')
+        ],
+        'salmonidx_gencode': [
+            clihelp: 'This flag will expect the input transcript FASTA ' +
+                'to be in GENCODE format, and will split the transcript ' +
+                'name at the first `|` character. These reduced names ' +
+                'will be used in the output and when looking for these ' +
+                'transcripts in a gene to transcript GTF.' +
+                " Default: ${params.salmonidx_gencode}",
+            cliflag: '--gencode',
+            clivalue: (params.salmonidx_gencode ? ' ' : '')
+        ],
+        'salmonidx_features': [
+            clihelp: 'This flag will expect the input reference to be in the ' +
+                'tsv file format, and will split the feature name at the first ' +
+                '`tab` character. These reduced names will be used in the output ' +
+                'and when looking for the sequence of the features. GTF.' +
+                " Default: ${params.salmonidx_features}",
+            cliflag: '--features',
+            clivalue: (params.salmonidx_features ? ' ' : '')
+        ],
+        'salmonidx_keepDuplicates': [
+            clihelp: 'This flag will disable the default indexing behavior of ' +
+                'discarding sequence-identical duplicate transcripts. If this ' +
+                'flag is passed then duplicate transcripts that appear in the ' +
+                'input will be retained and quantified separately.' +
+                " Default: ${params.salmonidx_keepDuplicates}",
+            cliflag: '--keepDuplicates',
+            clivalue: (params.salmonidx_keepDuplicates ? ' ' : '')
+        ],
+        'salmonidx_keepFixedFasta': [
+            clihelp: 'Retain the fixed fasta file (without short ' +
+                'transcripts and duplicates, clipped, etc.) generated ' +
+                "during indexing. Default: ${params.salmonidx_keepFixedFasta}",
+            cliflag: '--keepFixedFasta',
+            clivalue: (params.salmonidx_keepFixedFasta ?: '')
+        ],
+        'salmonidx_filterSize': [
+            clihelp: 'The size of the Bloom filter that will be used ' +
+                'by TwoPaCo during indexing. The filter will be of ' +
+                'size 2^{filterSize}. A value of -1 means that the ' +
+                'filter size will be automatically set based on the ' +
+                'number of distinct k-mers in the input, as estimated by ' +
+                "nthll. Default: ${params.salmonidx_filterSize}",
+            cliflag: '--filterSize',
+            clivalue: (params.salmonidx_filterSize ?: '')
+        ],
+        'salmonidx_sparse': [
+            clihelp: 'Build the index using a sparse sampling of k-mer ' +
+                'positions This will require less memory (especially ' +
+                'during quantification), but will take longer to construct' +
+                'and can slow down mapping / alignment.' +
+                " Default: ${params.salmonidx_sparse}",
+            cliflag: '--sparse',
+            clivalue: (params.salmonidx_sparse ? ' ' : '')
+        ],
+        'salmonidx_n': [
+            clihelp: 'Do not clip poly-A tails from the ends of target ' +
+                "sequences. Default: ${params.salmonidx_n}",
+            cliflag: '-n',
+            clivalue: (params.salmonidx_n ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file