Merge pull request #187 from joannakraw/fix-cutadapt-error

Fix No such variable: CUTADAPT error by replacing CUTADAPT.out with C…
nf-core · Jul 25, 2024 · 71676e6 · 71676e6
2 parents 5cfc4ee + 1da7769
commit 71676e6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Fix cutadapt 3' and 5' no such variable found bug ([#187](https://github.com/nf-core/crisprseq/pull/187))
+
 ### Deprecated
 
 ## [v2.2.1 Romarin Curie - patch](https://github.com/nf-core/crisprseq/releases/tag/2.2.1) - [23.07.2024]

diff --git a/README.md b/README.md
@@ -132,6 +132,7 @@ We thank the following people for their extensive assistance in the development
 - [@msanvicente](https://github.com/msanvicente)
 - [@mschaffer-incyte](https://github.com/mschaffer-incyte)
 - [@SusiJo](https://github.com/SusiJo)
+- [@joannakraw](https://github.com/joannakraw)
 
 ## Contributions and Support
 

diff --git a/workflows/crisprseq_screening.nf b/workflows/crisprseq_screening.nf
@@ -86,7 +86,7 @@ workflow CRISPRSEQ_SCREENING {
                 [meta, fastq, proto]
             }.set { ch_cutadapt }
 
-            ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT.out.log.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT_FIVE_PRIME.out.log.collect{it[1]})
             ch_versions = ch_versions.mix(CUTADAPT_FIVE_PRIME.out.versions)
         }
 
@@ -95,7 +95,7 @@ workflow CRISPRSEQ_SCREENING {
                 ch_cutadapt
             )
             ch_cutadapt = CUTADAPT_THREE_PRIME.out.reads.combine(Channel.value([[]]))
-            ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT.out.log.collect{it[1]})
+            ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT_THREE_PRIME.out.log.collect{it[1]})
             ch_versions = ch_versions.mix(CUTADAPT_THREE_PRIME.out.versions)
         }