From cd90ccd9bdfbf0ad293f603a5d112e17e17fd879 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luc=C3=ADa=20Pe=C3=B1a-P=C3=A9rez?=
 <lucia.pena.perez@scilifelab.se>
Date: Mon, 6 Nov 2023 10:26:49 +0100
Subject: [PATCH] Apply suggestions from code review

Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
---
 assets/multiqc_config.yml       | 2 +-
 nextflow.config                 | 2 +-
 subworkflows/local/alignment.nf | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 5851a9f3..179510d0 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/0.1.0" target="_blank">genomic-medicine-sweden/tomte</a>
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/1.0.0" target="_blank">genomic-medicine-sweden/tomte</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/output.md" target="_blank">documentation</a>.
 report_section_order:
diff --git a/nextflow.config b/nextflow.config
index 37486b4a..cbedd9f3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -252,7 +252,7 @@ manifest {
     description     = """Pipeline to analyse RNAseq from raredisease patients"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '0.1.0'
+    version = '1.0.0'
     doi             = ''
 }
 
diff --git a/subworkflows/local/alignment.nf b/subworkflows/local/alignment.nf
index 60e78379..b6f26f72 100644
--- a/subworkflows/local/alignment.nf
+++ b/subworkflows/local/alignment.nf
@@ -37,7 +37,7 @@ workflow ALIGNMENT {
         FASTP(ch_cat_fastq, [], false, false)
 
         ch_gtf = gtf.map { it -> [[:], it] }
-        STAR_ALIGN(FASTP.out.reads, star_index, ch_gtf, false, 'illumina', false)
+        STAR_ALIGN(FASTP.out.reads, star_index, ch_gtf, false, platform, false)
 
         SAMTOOLS_INDEX( STAR_ALIGN.out.bam )