Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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WES Preprocessing
Whole Exome Sequence analysis Preprocessing |
![]() Path: workflows/exomeseq-preprocessing.cwl Branch/Commit ID: 66b46c15d266fdf6a1faabd8d2f1b257f3438efc |
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merge and annotate svs with population allele freq and vep
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![]() Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5 |
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Scattered variant calling workflow
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![]() Path: WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl Branch/Commit ID: 2691061efa8341166ad6518688e5e6c0fb9a8fbf |
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allele-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. |
![]() Path: subworkflows/allele-alignreads-se-pe.cwl Branch/Commit ID: 915ea871cc28f7b666a4d7b476fdaa7b454ce7c3 |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files |
![]() Path: subworkflows/bam-bedgraph-bigwig.cwl Branch/Commit ID: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d |
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varscan somatic workflow
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![]() Path: definitions/subworkflows/varscan.cwl Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a |
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Production Configuration
This workflow prepares the configuration of the subsequent production steps. |
![]() Path: workflows/wms/uc-wms-XXX.cwl Branch/Commit ID: 76f7c25c0472da23b7e0bfe9f2c18ab6bc369c9d |
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scatter-wf4.cwl#main
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![]() Path: cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944 Packed ID: main |
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env-wf2.cwl
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![]() Path: tests/env-wf2.cwl Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3 |
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kmer_cache_store
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![]() Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: 9abcceb95c8dcb74b98d7eeda265d8f3a9a4329e |