Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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exomeseq-gatk4-01-preprocessing.cwl
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https://github.com/Duke-GCB/bespin-cwl.git
Path: subworkflows/exomeseq-gatk4-01-preprocessing.cwl Branch/Commit ID: 66b46c15d266fdf6a1faabd8d2f1b257f3438efc |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05 |
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vcf_concat.cwl
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https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/subworkflows/vcf_concat.cwl Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf |
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call_variants.cwl
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https://github.com/mskcc/ACCESS-Pipeline.git
Path: workflows/subworkflows/call_variants.cwl Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf |
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Seed Protein Alignments
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https://github.com/ncbi/pgap.git
Path: protein_alignment/wf_seed_1.cwl Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf |
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extract_gencoll_ids
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https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 16d1198871195e2229fd44dd0ad94a4ed6a87caf |
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Vcf concordance evaluation workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/vcf_eval_concordance.cwl Branch/Commit ID: 258bd4353ad1ca7790b3ae626bf42ab8194e7561 |
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strelka workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/strelka_and_post_processing.cwl Branch/Commit ID: 293dc7b83639d21a56efff2baf9dfe4e97b9b806 |
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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 |
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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 |
