Bugfix release 2.2.4 for mirtop gff issues

CHANGELOG.md

@@ -3,6 +3,10 @@
 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).
 
+## [v2.2.4](https://github.com/nf-core/smrnaseq/releases/tag/2.2.4) - 2023-09-07
+
+- Bugfix for issue with handling malformed GFF3 from mirbase (was forgotten in 2.2.3)
+
 ## [v2.2.3](https://github.com/nf-core/smrnaseq/releases/tag/2.2.3) - 2023-09-06
 
 - [[#271]](https://github.com/nf-core/smrnaseq/issues/271) - Bugfix for parsing hairpin and mature fasta files

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.3" target="_blank">nf-core/smrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/smrnaseq/2.2.4" target="_blank">nf-core/smrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/smrnaseq/2.2.3/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/smrnaseq/2.2.4/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-smrnaseq-methods-description":
     order: -1000

modules/local/mirtop_quant.nf

@@ -24,9 +24,12 @@ process MIRTOP_QUANT {
     script:
     def filter_species = params.mirgenedb ? params.mirgenedb_species : params.mirtrace_species
     """
-    mirtop gff --hairpin $hairpin --gtf $gtf -o mirtop --sps $filter_species ./bams/*
-    mirtop counts --hairpin $hairpin --gtf $gtf -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
-    mirtop export --format isomir --hairpin $hairpin --gtf $gtf --sps $filter_species -o mirtop mirtop/mirtop.gff
+    #Cleanup the GTF if mirbase html form is broken
+    GTF="$gtf"
+    sed 's/&gt;/>/g' \$GTF | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\\n*\$/{\$d;N;};/\\n\$/ba' > \${GTF}_html_cleaned.fa
+    mirtop gff --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species ./bams/*
+    mirtop counts --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa -o mirtop --sps $filter_species --add-extra --gff mirtop/mirtop.gff
+    mirtop export --format isomir --hairpin $hairpin --gtf \${GTF}_html_cleaned.fa --sps $filter_species -o mirtop mirtop/mirtop.gff
     mirtop stats mirtop/mirtop.gff --out mirtop/stats
     mv mirtop/stats/mirtop_stats.log mirtop/stats/full_mirtop_stats.log
 

modules/local/parse_fasta_mirna.nf

@@ -25,7 +25,7 @@ process PARSE_FASTA_MIRNA {
         gunzip -f \$FASTA
         FASTA=\${FASTA%%.gz}
     fi
-    sed 's/&gt;/>/g' \$FASTA | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' > \${FASTA}_html_cleaned.fa
+    sed 's/&gt;/>/g' \$FASTA | sed 's#<br>#\\n#g' | sed 's#</p>##g' | sed 's#<p>##g' | sed -e :a -e '/^\\n*\$/{\$d;N;};/\\n\$/ba' > \${FASTA}_html_cleaned.fa
     # Remove spaces from miRBase FASTA files
     sed '#^[^>]#s#[^AUGCaugc]#N#g' \${FASTA}_html_cleaned.fa > \${FASTA}_parsed.fa
 

nextflow.config

@@ -272,7 +272,7 @@ manifest {
     description     = """Small RNA-Seq Best Practice Analysis Pipeline."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '2.2.3'
+    version = '2.2.4'
     doi             = ''
 }