From 48222543dfe2ff9e149116d6aeb679e3d73c3f27 Mon Sep 17 00:00:00 2001
From: not populated not populated <ameynert@sdf-cs1.eidf.epcc.ed.ac.uk>
Date: Wed, 29 Sep 2021 13:45:28 +0100
Subject: [PATCH] Using Nextera read trimming for EdGe sequencing as well as
CRF - only need a single template & config file
---
...SOP_alignment_variant_annotation_ultra2.md | 2 +-
trio_whole_exome_bcbio_crf_template.yaml | 22 -------------------
trio_whole_exome_bcbio_template.yaml | 3 +++
trio_whole_exome_crf_config.sh | 21 ------------------
4 files changed, 4 insertions(+), 44 deletions(-)
delete mode 100644 trio_whole_exome_bcbio_crf_template.yaml
delete mode 100644 trio_whole_exome_crf_config.sh
diff --git a/docs/SOP_alignment_variant_annotation_ultra2.md b/docs/SOP_alignment_variant_annotation_ultra2.md
index 097facb..82a7090 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 e379642..0000000
--- 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 f6ebbb4..e379642 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 3b7a89f..0000000
--- 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
--
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