Move reference params back into main.nf

Fixes #121
nf-core · Nov 25, 2019 · 7ca82c4 · 7ca82c4
1 parent 4380233
commit 7ca82c4
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,7 @@
 
 ### Pipeline Updates
 
+* Fixed bug where the iGenomes config was loaded after the references were set ([#121](https://github.com/nf-core/methylseq/issues/121))
 * Removed awsbatch config profile because it is now served by [nf-core/configs](https://github.com/nf-core/configs)
 
 ## [v1.4](https://github.com/nf-core/methylseq/releases/tag/1.4) - 2019-11-19

diff --git a/main.nf b/main.nf
@@ -94,6 +94,12 @@ assert params.aligner == 'bwameth' || params.aligner == 'bismark' || params.alig
  * SET UP CONFIGURATION VARIABLES
  */
 
+// These params need to be set late, after the iGenomes config is loaded
+bismark_index = params.genome ? params.genomes[ params.genome ].bismark ?: false : false
+bwa_meth_index = params.genome ? params.genomes[ params.genome ].bwa_meth ?: false : false
+fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
+fasta_index = params.genome ? params.genomes[ params.genome ].fasta_index ?: false : false
+
 // Check if genome exists in the config file
 if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
     exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"

diff --git a/nextflow.config b/nextflow.config
@@ -13,10 +13,6 @@ params {
   reads = "data/*_R{1,2}.fastq.gz"
   single_end = false
   aligner = 'bismark'
-  bismark_index = params.genome ? params.genomes[ params.genome ].bismark ?: false : false
-  bwa_meth_index = params.genome ? params.genomes[ params.genome ].bwa_meth ?: false : false
-  fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
-  fasta_index = params.genome ? params.genomes[ params.genome ].fasta_index ?: false : false
   comprehensive = false
   ignore_flags = false
   meth_cutoff = false