1 数据：

参考基因（小数据）从/ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human截取前1000行：/ceph_disk2/app/tmp/test.fa

原始数据数据： /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human

镜像： images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0

SevenBridge CWL

1. https://igor.sbgenomics.com/public/apps/admin/sbg-public-data/bismark-analysis-0-19-0
2. https://igor.sbgenomics.com/public/apps/admin/sbg-public-data/bismark-methylation-extractor-0-21-0

2 命令

1. 
bismark_genome_preparation --path_to_aligner /opt/bowtie2-2.3.2-legacy/ --verbose /ceph_disk2/app/tmp

2.
bismark --genome /ceph_disk2/app/tmp /opt/Bismark/test_data.fastq

3. 
deduplicate_bismark --bam test_data_bismark_bt2.bam
4. 
bismark_methylation_extractor --gzip --bedGraph test_data_bismark_bt2.bam
5.
bismark2report