diff --git a/docs/SOP_alignment_variant_annotation_ultra2.md b/docs/SOP_alignment_variant_annotation_ultra2.md
index 097facbc5b7c9b5ff4c2e0393cf40a3c5ac38d0a..82a70900cc7438e859f3c08a52dfd765646e727f 100644
--- a/docs/SOP_alignment_variant_annotation_ultra2.md
+++ b/docs/SOP_alignment_variant_annotation_ultra2.md
@@ -82,7 +82,7 @@ A [configuration script](../trio_whole_exome_config.sh) sets environment variabl
 
 ## Template for bcbio configuration
 
-Bcbio requires a [template file in YAML format](../trio_whole_exome_bcbio_template.yaml). to define the procedures run in the pipeline. Runs from the Edinburgh CRF have a [slightly different template file](../trio_whole_exome_bcbio_crf_template.yaml) which adds read trimming parameters specific to NextSeq 2000 output.
+Bcbio requires a [template file in YAML format](../trio_whole_exome_bcbio_template.yaml). to define the procedures run in the pipeline.
 
 ## Output
 
diff --git a/trio_whole_exome_bcbio_crf_template.yaml b/trio_whole_exome_bcbio_crf_template.yaml
deleted file mode 100644
index e379642d408852e6aff9309fbc3be6ae0502a6ff..0000000000000000000000000000000000000000
--- a/trio_whole_exome_bcbio_crf_template.yaml
+++ /dev/null
@@ -1,22 +0,0 @@
-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: /scratch/u035/u035/shared/trio_whole_exome/analysis/output
diff --git a/trio_whole_exome_bcbio_template.yaml b/trio_whole_exome_bcbio_template.yaml
index f6ebbb44f3e55484bf6eab03decdbf5ecb9263f6..e379642d408852e6aff9309fbc3be6ae0502a6ff 100644
--- a/trio_whole_exome_bcbio_template.yaml
+++ b/trio_whole_exome_bcbio_template.yaml
@@ -3,6 +3,9 @@ details:
     platform: illumina
     quality_format: standard
     aligner: bwa
+    align_split_size: false
+    trim_reads: fastp
+    adapters: [nextera2, polyg]
     mark_duplicates: true
     realign: false
     recalibrate: true
diff --git a/trio_whole_exome_crf_config.sh b/trio_whole_exome_crf_config.sh
deleted file mode 100644
index 3b7a89fdf2e885ce50a550b089645f45c9bcd194..0000000000000000000000000000000000000000
--- a/trio_whole_exome_crf_config.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/bash
-#
-# Basic configuration options for trio WES pipeline
-#
-
-SCRIPTS=/home/u035/u035/shared/scripts
-BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_crf_template.yaml
-TARGET=/home/u035/u035/shared/resources/exome_targets/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
-DOWNLOAD_DIR=/scratch/u035/u035/shared/data
-REFERENCE_GENOME=/home/u035/u035/shared/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
-
-BASE=/scratch/u035/u035/shared/analysis
-PARAMS_DIR=$BASE/params
-READS_DIR=$BASE/reads
-CONFIG_DIR=$BASE/config
-WORK_DIR=$BASE/work
-OUTPUT_DIR=$BASE/output
-
-ARCHIVE_DIR=/archive/u035/trio_whole_exome
-
-export PATH=/home/u035/u035/shared/software/bcbio/tools/bin:$PATH