better sanitisation of ref seq IDs [CW-3411]

CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [unreleased]
+### Fixed
+- The workflow failing when there were tab characters in the FASTA header lines of reference sequences.
+
+### Changed
+- The way the reference sequence IDs are sanitised to prevent issues with special characters.
+
 ## [v1.0.3]
 ### Fixed
 - The workflow failing when there was a whitespace in the name of the reference file.

modules/local/variant-calling.nf

@@ -18,7 +18,9 @@ process sanitizeRefFile {
     output: path "reference_sanitized_seqIDs.fasta"
     script:
     """
-    sed '/^>/s/:\\|\\*\\| /_/g' reference.fasta > reference_sanitized_seqIDs.fasta
+    # use `sed` to replace all non-alphanumerical characters with underscores (`/2g`
+    # skips the first match which will be `>`)
+    sed -E '/^>/s/[^[:alnum:]]+/_/2g' reference.fasta > reference_sanitized_seqIDs.fasta
     """
 }
 
@@ -175,8 +177,11 @@ workflow pipeline {
         // subset the sanitized ref file
         ref_id_map = Channel.empty()
         | concat(
-            Channel.of(ref).splitFasta(record: [id: true]).map{ it.id }.collect(),
-            san_ref.splitFasta(record: [id: true]).map{ it.id }.collect()
+            // `splitFasta(reecord: [id: true])` does not split the header line at tab
+            // characters. We thus split again here to make sure that we only got the
+            // seq ID
+            Channel.of(ref).splitFasta(record: [id: true]).map{ it.id.split()[0] }.collect(),
+            san_ref.splitFasta(record: [id: true]).map{ it.id.split()[0] }.collect()
         )
         | toList
         | map { it.transpose().collectEntries() as LinkedHashMap }