Merge pull request #419 from apeltzer/fix-igenomes

Fix #418 (iGenomes GRCm38 paths)
nf-core · Oct 10, 2019 · 2358cdb · 2358cdb
2 parents 2e2fe8e + 514dac6
commit 2358cdb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,10 @@
 
 * Updated Base Dockerfile to Conda 4.7.10
 
+### Template
+
+* Fixed incorrect paths in iGenomes config as described in issue [418](https://github.com/nf-core/tools/issues/418)
+
 ## v1.7
 
 ### PyPI package description

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/igenomes.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/igenomes.config
@@ -24,8 +24,8 @@ params {
       fasta   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
       gtf     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
       star    = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/"
-      bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCh37/Sequence/Bowtie2Index/"
-      bwa     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCh37/Sequence/BWAIndex/"
+      bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/"
+      bwa     = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/"
     }
     'TAIR10' {
       bed12   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"