Fixing bcbio template, removing test duplicate

bin/trio_whole_exome_bcbio_template.yaml → assets/trio_whole_exome_bcbio_template.yaml

@@ -19,4 +19,5 @@ details:
   analysis: variant2
   genome_build: hg38
 upload:
-  dir: /home/u035/u035/shared/results
+  # relative path will output locally to the bcbio run folder
+  dir: ./results 

nextflow.config

@@ -7,6 +7,8 @@ params {
     min_cpus = 1
     min_mem = 1.GB
     min_time = 2.h
+
+    bcbio_template = "$projectDir/assets/trio_whole_exome_bcbio_template.yaml"
 }
 
 
@@ -25,11 +27,10 @@ profiles {
         params.max_mem = 1.GB
         params.max_time = 1.h
 
-        params.bcbio = 'scripts/bcbio_nextgen.py'
-        params.bcbio_template = 'assets/bcbio/bcbio_template.yaml'
-        params.target_bed = 'assets/input_data/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed'
-        params.reference_genome = 'assets/ref.fa'
-        params.output_dir = 'outputs'
+        params.bcbio = "$projectDir/tests/scripts/bcbio_nextgen.py"
+        params.target_bed = "$projectDir/tests/assets/input_data/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed"
+        params.reference_genome = "$projectDir/tests/assets/ref.fa"
+        params.output_dir = "$projectDir/tests/outputs"
     }
 
     slurm {

tests/assets/bcbio/bcbio_template.yaml

-details:
-- algorithm:
-    platform: illumina
-    quality_format: standard
-    aligner: bwa
-    align_split_size: false
-    trim_reads: fastp
-    adapters: [nextera2, polyg]
-    mark_duplicates: true
-    realign: false
-    recalibrate: true
-    effects: vep
-    effects_transcripts: all
-    variantcaller: gatk-haplotype
-    indelcaller: false
-    remove_lcr: true
-    tools_on:
-    - vep_splicesite_annotations
-  analysis: variant2
-  genome_build: hg38
-upload:
-  dir: outputs/bcbio/results