CWL run of Alignment Workflow (CWLProv 0.6.0 Research Object)

The CWL alignment workflow included in this case study is designed by Data Biosphere. It adapts the alignment pipeline originally developed at Abecasis Lab, The University of Michigan. This workflow is part of NIH Data Commons initiative and comprises of four stages. First step, "Pre-align'' accepts a Compressed Alignment Map (CRAM) file (a compressed format for BAM files developed by European Bioinformatics Institute (EBI)) and human genome reference sequence as input and using underlying software utilities of SAMtools such as view, sort and fixmate returns a list of fastq files which can be used as input for the next step. The next step "Align'' also accepts the human reference genome as input along with the output files from "Pre-align'' and uses BWA-mem to generate aligned reads as BAM files. SAMBLASTER is used to mark duplicate reads and SAMtools view to convert read files from SAM to BAM format. The BAM files generated after "Align'' are sorted with "SAMtool sort''. Finally, these sorted alignment files are merged to produce single sorted BAM file using SAMtools merge in "Post-align'' step. This dataset folder is a CWLProv Research Object that captures the Common Workflow Language execution provenance, see https://w3id.org/cwl/prov/0.6.0 or use https://pypi.org/project/cwlprov/ to explore本案例研究所采用的通用工作流语言（Common Workflow Language，CWL）比对工作流由Data Biosphere设计，其适配了密歇根大学Abecasis实验室最初开发的基因组比对流程。本工作流隶属于美国国立卫生研究院（National Institutes of Health，NIH）数据共同体计划，共包含四个执行阶段。 第一阶段"预比对（Pre-align）"以压缩比对映射文件（Compressed Alignment Map，CRAM，欧洲生物信息研究所（EBI）开发的BAM文件专用压缩格式）与人类基因组参考序列作为输入，依托SAMtools的view、sort及fixmate等子命令工具，输出可用于下一阶段的fastq文件列表。 第二阶段"比对（Align）"同样以人类基因组参考序列为输入，并结合"预比对"阶段的输出文件，通过BWA-mem算法生成比对后的读取序列并保存为BAM格式文件。其间使用SAMBLASTER标记重复读取序列，再通过SAMtools view工具将SAM格式的读取文件转换为BAM格式。 "比对"阶段生成的BAM文件将通过SAMtools sort完成排序。最终在"后比对（Post-align）"阶段，借助SAMtools merge工具将所有已排序的比对文件合并为单个已排序的BAM文件。 本数据集文件夹属于CWLProv研究对象，用于记录通用工作流语言的执行溯源信息，可访问https://w3id.org/cwl/prov/0.6.0 或通过https://pypi.org/project/cwlprov/ 进行探索。