diff --git a/conf/test_full.config b/conf/test_full.config index 8532e0d..3a2d38e 100644 --- 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 index 99c35e5..82267f7 100644 --- 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 }