From 9a8c93cf4dce775989a7a73a437585a3bda43156 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alex.peltzer@gmail.com>
Date: Mon, 14 Oct 2024 09:06:50 +0000
Subject: [PATCH] Tiny bugfixes

---
 .gitignore                                       |  2 ++
 CITATIONS.md                                     |  1 -
 nextflow.config                                  |  2 --
 .../local/utils_nfcore_smrnaseq_pipeline/main.nf | 16 ++++++++--------
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/.gitignore b/.gitignore
index a42ce016..24fc8b91 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,3 +7,5 @@ testing/
 testing*
 *.pyc
 null/
+execution_trace*
+.nf-test*
diff --git a/CITATIONS.md b/CITATIONS.md
index 99535fc7..f473604a 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -38,7 +38,6 @@
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
-> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 - [Bioconductor](https://www.bioconductor.org/) and [R](https://cran.r-project.org/)
diff --git a/nextflow.config b/nextflow.config
index c45ce2f9..e4f0e71e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -90,8 +90,6 @@ params {
     help                         = false
     help_full                    = false
     show_hidden                  = false
-    help_full                    = false
-    show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
     // Config options
diff --git a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
index bda2a7cf..c1494948 100644
--- a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
@@ -94,7 +94,7 @@ workflow PIPELINE_INITIALISATION {
         .groupTuple()
         .map { samplesheet ->
             validateInputSamplesheet(samplesheet)
-            }
+        }
         .map {
             meta, fastqs ->
                 return [ meta, fastqs.flatten() ]
@@ -170,34 +170,34 @@ def validateInputParameters() {
     genomeExistsError()
 
     if (!params.mirgenedb && !params.mirtrace_species) {
-            error("Reference species for miRTrace is not defined via the --mirtrace_species parameter.")
+            error("Reference species for miRTrace is not defined via the `--mirtrace_species` parameter.")
     }
 
     if (!params.mirgenedb) {
         // Validate mature miRNA fasta file
         if (!params.mature) {
-            error("Mature miRNA fasta file not found. Please specify using the '--mature' parameter.")
+            error("Mature miRNA fasta file not found. Please specify using the `--mature` parameter.")
         }
         // Validate hairpin miRNA fasta file
         if (!params.hairpin) {
-            error("Hairpin miRNA fasta file not found. Please specify using the '--hairpin' parameter.")
+            error("Hairpin miRNA fasta file not found. Please specify using the `--hairpin` parameter.")
         }
     } else {
         // Validate MirGeneDB species
         if (!params.mirgenedb_species) {
-            error("You specified to be using MirGeneDB, but the MirGeneDB species is not set. Please specify using the '--mirgenedb_species' parameter.")
+            error("You specified to be using MirGeneDB, but the MirGeneDB species is not set. Please specify using the `--mirgenedb_species` parameter.")
         }
         // Validate MirGeneDB mature miRNA fasta file
         if (!params.mirgenedb_mature) {
-            error("You specified to be using MirGeneDB, but the mature miRNA fasta file is not found. Please provide the file using the '--mirgenedb_mature' parameter.")
+            error("You specified to be using MirGeneDB, but the mature miRNA fasta file is not found. Please provide the file using the `--mirgenedb_mature` parameter.")
         }
         // Validate MirGeneDB hairpin miRNA fasta file
         if (!params.mirgenedb_hairpin) {
-            error("You specified to be using MirGeneDB, but the hairpin miRNA fasta file is not found. Please provide the file using the '--mirgenedb_hairpin' parameter.")
+            error("You specified to be using MirGeneDB, but the hairpin miRNA fasta file is not found. Please provide the file using the `--mirgenedb_hairpin` parameter.")
         }
         // Validate MirGeneDB GFF file
         if (!params.mirgenedb_gff) {
-            error("You specified to be using MirGeneDB, but the GFF file is not found. Please provide the file using the '--mirgenedb_gff' parameter.")
+            error("You specified to be using MirGeneDB, but the GFF file is not found. Please provide the file using the `--mirgenedb_gff` parameter.")
         }
     }
 }