Links rather than text copy for config files and bcbio templates

docs/SOP_alignment_variant_annotation_ultra2.md

@@ -78,55 +78,11 @@ The project working directories will be in the folder `/home/u035/u035/shared/an
 
 ## Project configuration
 
-A configuration script sets environment variables common to scripts used in this SOP. This is stored at `/home/u035/u035/shared/scripts/trio_whole_exome_config.sh`.
-
-```
-#!/usr/bin/bash
-#
-# Basic configuration options for trio WES pipeline
-#
-
-BASE=/home/u035/u035/shared
-SCRIPTS=$BASE/scripts
-BCBIO_TEMPLATE=$SCRIPTS/trio_whole_exome_bcbio_template.yaml
-TARGET=$BASE/resources/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
-DOWNLOAD_DIR=$BASE/data
-REFERENCE_GENOME=$BASE/software/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa
-
-PARAMS_DIR=$BASE/analysis/params
-READS_DIR=$BASE/analysis/reads
-CONFIG_DIR=$BASE/analysis/config
-WORK_DIR=$BASE/analysis/work
-OUTPUT_DIR=$BASE/analysis/results
-
-export PATH=$BASE/software/bcbio/tools/bin:$PATH
-````
+A [configuration script](../trio_whole_exome_config.sh) sets environment variables common to scripts used in this SOP.
 
 ## Template for bcbio configuration
 
-Bcbio requires a template file in YAML format to define the procedures run in the pipeline. The template for this project is stored at `/home/u035/u035/shared/scripts/trio_whole_exome_bcbio_template.yaml`.
-
-```
-details:
-- algorithm:
-    platform: illumina
-    quality_format: standard
-    aligner: bwa
-    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: /home/u035/u035/shared/results
-```
+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.
 
 ## Output