Explore Workflows

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Graph Name Retrieved From View
workflow graph Vcf concordance evaluation workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/vcf_eval_concordance.cwl

Branch/Commit ID: 258bd4353ad1ca7790b3ae626bf42ab8194e7561
workflow graph strelka workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: 293dc7b83639d21a56efff2baf9dfe4e97b9b806
workflow graph allele-vcf-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

https://github.com/datirium/workflows.git

Path: subworkflows/allele-vcf-alignreads-se-pe.cwl

Branch/Commit ID: 2768d117212e50859edebea74b0641dfaf4feba4
workflow graph allele-vcf-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

https://github.com/datirium/workflows.git

Path: subworkflows/allele-vcf-alignreads-se-pe.cwl

Branch/Commit ID: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d
workflow graph Filter single sample sv vcf from paired read callers(Manta/Smoove)

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05
workflow graph Filter single sample sv vcf from depth callers(cnvkit/cnvnator)

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/sv_depth_caller_filter.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05
workflow graph fp_filter workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: 293dc7b83639d21a56efff2baf9dfe4e97b9b806
workflow graph Run genomic CMsearch

https://github.com/ncbi/pgap.git

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: 91181df8d9ef8eed9d8f40db707b9a4376fecaf5
workflow graph allele-process-strain.cwl

https://github.com/datirium/workflows.git

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 3b2e0de49d9ee6fd9a8c9580b6a02d0f7e4c8f7c
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 3034168d652bfa930ba09af20e473a4564a8010d