Merge pull request #36 from nf-core/lpantano-patch-i35

make sure one file is used in collapse step

CHANGELOG.md

@@ -1,8 +1,5 @@
 # nf-core/smrnaseq: Changelog
 
-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).
-
 ## v1.1dev - [date]
 
 * Change `--reads` to `--input` for consistency with rest of nf-core
@@ -17,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * Update with the latest `TEMPLATE` version for nf-core `v1.11`
 * Update conda environment with new packages and updates
 * Added `--protocol custom` to allow custom adapter trimming modes [[#41]](https://github.com/nf-core/smrnaseq/issues/41)]
+* Fix error when UMI is on the reads header: [[#35](https://github.com/nf-core/smrnaseq/issues/35)]
 
 ### Packaged software updates
 

main.nf

@@ -452,13 +452,14 @@ process collapse {
     file reads from trimmed_reads_collapse
 
     output:
-    file 'collapsed/*.fastq' into collapsed_fasta
+    file 'final/*.fastq' into collapsed_fasta
 
     script:
     prefix = reads.toString() - '_trimmed.fq.gz'
     """
     seqcluster collapse -f $reads -m 1 --min_size 15 -o collapsed
-    mv collapsed/${prefix}_trimmed_trimmed.fastq collapsed/${prefix}.fastq
+    mkdir final
+    mv collapsed/${prefix}_trimmed_trimmed.fastq final/${prefix}.fastq
     """
 }