update fai file for the full test and formating

sanger-tol · Nov 2, 2023 · 3e8705c · 3e8705c
1 parent d6fa00f
commit 3e8705c
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -23,6 +23,5 @@ params {
     fasta = '/lustre/scratch124/tol/projects/darwin/data/insects/Cantharis_rufa/assembly/release/icCanRufa1.1/insdc/GCA_947369205.1.fasta.gz'
 
     // Reference index file
-    fai = '/lustre/scratch124/tol/projects/darwin/data/insects/Cantharis_rufa/assembly/release/icCanRufa1.1/insdc/GCA_947369205.1.fasta.gz.fai'
-    gzi = '/lustre/scratch124/tol/projects/darwin/data/insects/Cantharis_rufa/assembly/release/icCanRufa1.1/insdc/GCA_947369205.1.fasta.gz.gzi'
+    fai = '/lustre/scratch124/tol/projects/darwin/data/insects/Cantharis_rufa/assembly/release/icCanRufa1.1/insdc/GCA_947369205.1.fasta.gz.gzi'
 }
diff --git a/workflows/variantcalling.nf b/workflows/variantcalling.nf
@@ -25,10 +25,11 @@ if (params.fai){
     ){
       exit 1, 'Reference fasta and its index file format not matched!'
     }
-    ch_fai   = Channel.fromPath(params.fai)
+    ch_fai = Channel.fromPath(params.fai)
 } else { 
-    ch_fai      = Channel.empty() 
+    ch_fai = Channel.empty()
 }
+
 if (params.interval){ ch_interval = Channel.fromPath(params.interval) } else { ch_interval = Channel.empty() }
 
 if (params.split_fasta_cutoff ) { split_fasta_cutoff = params.split_fasta_cutoff } else { split_fasta_cutoff = 100000 }