From 79a4bec16d1bede81cc14fc3151c7ee664987b97 Mon Sep 17 00:00:00 2001
From: Matt Parker <matt.parker@nanoporetech.com>
Date: Thu, 26 May 2022 08:27:38 +0100
Subject: [PATCH] Zero hour 9:00 a.m.

---
 CHANGELOG.md            | 14 ++++++++------
 lib/WorkflowMain.groovy |  8 ++++++--
 nextflow.config         | 10 +++++++++-
 3 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b79e883..53f6ce1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,11 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [unreleased]
+### Changed
+- Better help text on cli
+
 ## [v0.1.2]
-### Added 
+### Added
 - direct_rna option
 - Some extra error handling
-- Minor report display improvements 
+- Minor report display improvements
 
 ## [v0.1.1]
 ### Fixed
@@ -17,8 +21,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Several small fixes in report plotting
 
 ## [v0.1.0]
-### Added 
-- Added the denovo pipeline 
+### Added
+- Added the denovo pipeline
 ### Changed
 - Updates to the report plots
 
@@ -26,5 +30,3 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - First release
 - Initial port of Snakemake WF from https://github.com/nanoporetech/pipeline-nanopore-ref-isoforms
-
-
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index fce9181..c518e53 100644
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -1,16 +1,20 @@
+// This file is based on the nf-core/tools pipeline-template.
+// Changes to this file must be propagated via wf-template.
 
 class WorkflowMain {
 
     // Citation string for pipeline
     public static String citation(workflow) {
-        return "If you use wf-template for your analysis please cite:\n\n" +
+        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
             "* The nf-core framework\n" +
             "  https://doi.org/10.1038/s41587-020-0439-x\n\n"
     }
 
     // Print help to screen
     public static String help(workflow, params, log) {
-        def command = "nextflow run epi2me-labs/wf-template --fastq <input folder> -profile docker"
+        String line_sep = ' \\ \n\t'
+        def command_example = params.wf.example_cmd.join(line_sep)
+        def command = 'nextflow run ' + workflow.manifest.name + line_sep + command_example
         def help_string = ''
         help_string += NfcoreSchema.paramsHelp(workflow, params, command)
         help_string += '\n' + citation(workflow) + '\n'
diff --git a/nextflow.config b/nextflow.config
index f4b52c6..8fae2b1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -53,7 +53,7 @@ params {
     // Internal priming filter context size:
     poly_context = 24
 
-    // Maximum allowed poly(A) length in the genome near the 3' end of mapping: 
+    // Maximum allowed poly(A) length in the genome near the 3' end of mapping:
     max_poly_run = 8
 
     // Minimium number of reads in BAM bundles:
@@ -118,6 +118,14 @@ params {
     // Minimum probability for i consecutive minimizers to be different between read and representative:
     min_prob_no_hits = 0.1
 
+    wf {
+      example_cmd = [
+          "--fastq test_data/fastq",
+          "--ref_genome test_data/SIRV_150601a.fasta",
+          "--ref_annotation test_data/SIRV_isofroms.gtf"
+      ]
+    }
+
 
 }