--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/lib/help/medakaconsensus.nf	Thu May 28 20:41:10 2026 +0000
@@ -0,0 +1,102 @@
+// Help text for medaka `consensus` within CPIPES.
+
+def medakaconsensusHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'medakaconsensus_run': [
+            clihelp: 'Run medaka `consensus` tool. Default: ' +
+                (params.medakaconsensus_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'medakaconsensus_batch_size': [
+            clihelp: 'Inference batch size. ' +
+                "Default: ${params.medakaconsensus_batch_size}",
+            cliflag: '--batch_size',
+            clivalue: (params.medakaconsensus_batch_size ?: '')
+        ], 
+        'medakaconsensus_chunk_len': [
+            clihelp: 'Chunk length of samples. ' +
+                "Default: ${params.medakaconsensus_chunk_len}",
+            cliflag: '--chunk_len',
+            clivalue: (params.medakaconsensus_chunk_len ?: '')
+        ],
+        'medakaconsensus_chunk_ovlp': [
+            clihelp: 'Overlap of chunks. ' +
+                "Default: ${params.medakaconsensus_chunk_ovlp}",
+            cliflag: '--chunk_ovlp',
+            clivalue: (params.medakaconsensus_chunk_ovlp ?: '')
+        ],
+        'medakaconsensus_regions': [
+            clihelp: 'Genomic regions to analyze, or a bed file. ' +
+                "Default: ${params.medakaconsensus_regions}",
+            cliflag: '--regions',
+            clivalue: (params.medakaconsensus_regions ?: '')
+        ],
+        'medakaconsensus_model': [
+            clihelp: 'Model to use. Can be a medaka model name or a basecaller model name ' +
+                "suffixed with ':consensus' or ':variant'. " +
+                "Ex: 'dna_r10.4.1_e8.2_400bps_hac@v4.1.0:variant'. " +
+                "Default: ${params.medakaconsensus_model}",
+            cliflag: '--model',
+            clivalue: (params.medakaconsensus_model ?: '')
+        ],
+        'medakaconsensus_auto_model': [
+            clihelp: 'Automatically choose model according to input. Use one of ' +
+                "'consensus' or 'variant'. Default: ${params.medakaconsensus_auto_model}",
+            cliflag: '--auto_model',
+            clivalue: (params.medakaconsensus_auto_model ?: '')
+        ],
+        'medakaconsensus_bam_chunk': [
+            clihelp: 'Size of reference chunks each worker parses from bam. ' +
+                "Default: ${params.medakaconsensus_bam_chunk}",
+            cliflag: '--bam_chunk',
+            clivalue: (params.medakaconsensus_bam_chunk ?: '')
+        ],
+        'medakaconsensus_chk_out': [
+            clihelp: 'Verify integrity of output file after inference. ' +
+                "Default: ${params.medakaconsensus_chk_out}",
+            cliflag: '--check_output',
+            clivalue: (params.medakaconsensus_chk_out ? ' ' : '')
+        ],
+        'medakaconsensus_save_feats': [
+            clihelp: 'Save features with consensus probabilities. ' +
+                "Default: ${params.medakaconsensus_save_feats}",
+            cliflag: '--save_features',
+            clivalue: (params.medakaconsensus_save_feats ? ' ' : '')
+        ],
+        'medakaconsensus_read_grp': [
+            clihelp: "Read group to select. Default: ${params.medakaconsensus_read_grp}",
+            cliflag: '--RG',
+            clivalue: (params.medakaconsensus_read_grp ?: '')
+        ],
+        'medakaconsensus_tag_name': [
+            clihelp: "Two-letter tag name. Default: ${params.medakaconsensus_tag_name}",
+            cliflag: '--tag_name',
+            clivalue: (params.medakaconsensus_tag_name ?: '')
+        ],
+        'medakaconsensus_tag_val': [
+            clihelp: "Value of tag. Default: ${params.medakaconsensus_tag_val}",
+            cliflag: '--tag_val',
+            clivalue: (params.medakaconsensus_tag_val ?: '')
+        ],
+        'medakaconsensus_tag_keep': [
+            clihelp: 'Keep alignments when tag is missing. '
+            + "Default: ${params.medakaconsensus_tag_keep}",
+            cliflag: '--tag_keep_missing',
+            clivalue: (params.medakaconsensus_tag_keep ?: '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file