Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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Apply filters to VCF file
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![]() Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: 742dbafb5fb103d8578f48a0576c14dd8dae3b2a |
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Add snv and indel bam-readcount files to a vcf
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![]() Path: definitions/subworkflows/vcf_readcount_annotator.cwl Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0 |
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metabarcode (gene amplicon) analysis for fastq files
protein - qc, preprocess, annotation, index, abundance |
![]() Path: CWL/Workflows/metabarcode-fastq.workflow.cwl Branch/Commit ID: 7b1df2ecce5a8727f2c546c5baa45c919edd8a76 |
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Gathered Downsample and HaplotypeCaller
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![]() Path: definitions/pipelines/gathered_downsample_and_recall.cwl Branch/Commit ID: 06d2440d115b446c299b4ce96e8812d2f8df86ec |
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functional-wf.cwl
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![]() Path: tests/checker_wf/functional-wf.cwl Branch/Commit ID: 84939620c3eec1ab11369849c63237ebfa48da41 |
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Raw sequence data to BQSR
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![]() Path: definitions/subworkflows/sequence_to_bqsr.cwl Branch/Commit ID: 06d2440d115b446c299b4ce96e8812d2f8df86ec |
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wf_clipseqcore_pe_2barcodes.cwl
Workflow for handling reads containing two barcodes. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs |
![]() Path: cwl/wf_clipseqcore_pe_2barcodes.cwl Branch/Commit ID: 6b533898c395e9e5b9d0acc1587d0c68bc56abe0 |
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wf_trim_and_map_se.cwl
This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment |
![]() Path: cwl/wf_trim_and_map_se.cwl Branch/Commit ID: 6b533898c395e9e5b9d0acc1587d0c68bc56abe0 |
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Subworkflow to allow calling different SV callers which require bam files as inputs
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![]() Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: 700e73aaed6db1ad538dd27b2e1709f436ad3edb |
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Dockstore.cwl
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![]() Path: Dockstore.cwl Branch/Commit ID: fe907a47040554f3e77694e02313321b0f64f265 |