Explore Workflows

creates genome coverage bigWig file from .bam file

https://github.com/barski-lab/ga4gh_challenge.git

Path: workflows/bam-genomecov-bigwig.cwl

Branch/Commit ID: v0.0.2

Some workflow engines won't stage files in our nested structure, so parse it out here

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl

Branch/Commit ID: low-vaf

This is a very simple workflow of two steps. It will zip an input VCF file and then index it. The zipped file and the index file will be in the workflow output.

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: zip_and_index_vcf.cwl

Branch/Commit ID: develop

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-assembly.cwl

Branch/Commit ID: master

https://github.com/kyusque/abmp_log_dump2pieda.git

Path: test-extract_fraginfo.cwl

Branch/Commit ID: master

https://github.com/kids-first/kf-rnaseq-workflow.git

Path: workflow/kfdrc_flagstat_qc.cwl

Branch/Commit ID: master

{'extract_fastq': 'http://218.77.58.141:9619','extract_fastq2': 'http://218.77.58.141:9619','extract_fastq3': 'http://121.46.19.86:9619','extract_fastq4': 'http://121.46.19.86:9619', 'fastx_quality_stats': 'http://218.77.58.141:9619','fastx_quality_stats2': 'http://218.77.58.141:9619','fastx_quality_stats3': 'http://121.46.19.86:9619','fastx_quality_stats4': 'http://121.46.19.86:9619','bowtie_aligner': 'http://218.77.58.141:9619','bowtie_aligner2': 'http://218.77.58.141:9619', 'bowtie_aligner3': 'http://121.46.19.86:9619', 'bowtie_aligner4': 'http://121.46.19.86:9619', 'samtools_sort_index': 'http://218.77.58.141:9619','samtools_sort_index2': 'http://218.77.58.141:9619','samtools_sort_index3': 'http://121.46.19.86:9619','samtools_sort_index4': 'http://121.46.19.86:9619', 'samtools_rmdup': 'http://218.77.58.141:9619', 'samtools_rmdup2': 'http://218.77.58.141:9619', 'samtools_rmdup3': 'http://121.46.19.86:9619', 'samtools_rmdup4': 'http://121.46.19.86:9619', 'samtools_sort_index_after_rmdup': 'http://218.77.58.141:9619', 'samtools_sort_index_after_rmdup2': 'http://218.77.58.141:9619', 'samtools_sort_index_after_rmdup3': 'http://121.46.19.86:9619', 'samtools_sort_index_after_rmdup4': 'http://121.46.19.86:9619', 'macs2_callpeak': 'http://218.77.58.141:9619', 'macs2_callpeak2': 'http://218.77.58.141:9619','macs2_callpeak3': 'http://121.46.19.86:9619','macs2_callpeak4': 'http://121.46.19.86:9619', 'get_stat': 'http://218.77.58.141:9619', 'get_stat2': 'http://218.77.58.141:9619', 'get_stat3': 'http://121.46.19.86:9619', 'get_stat4': 'http://121.46.19.86:9619', 'island_intersect': 'http://218.77.58.141:9619', 'island_intersect2': 'http://218.77.58.141:9619', 'island_intersect3': 'http://121.46.19.86:9619', 'island_intersect4': 'http://121.46.19.86:9619', 'average_tag_density': 'http://218.77.58.141:9619', 'average_tag_density2': 'http://218.77.58.141:9619', 'average_tag_density3': 'http://121.46.19.86:9619', 'average_tag_density4': 'http://121.46.19.86:9619' }

https://github.com/liuzhiyonggd/ga4gh.git

Path: biowardrobe_chipseq_se.4.cwl

Branch/Commit ID: main

https://github.com/svonworl/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow.git

Path: broad-best-practice-data-pre-processing-workflow-4-1-0-0_decomposed.cwl

Branch/Commit ID: master

https://github.com/common-workflow-language/workflows.git

Path: workflows/GATK/GATK-Sub-Workflow-h3abionet-snp.cwl

Branch/Commit ID: h3abionet-gatk-workflow

https://github.com/ifishlin/Benchmarking_CWL.git

Path: workflows/methylCtools/tools/methylCtools_align_merge_sort_dedup.cwl

Branch/Commit ID: main