Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs. |
![]() Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7 |
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bwa_index
Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl |
![]() Path: structuralvariants/cwl/subworkflows/bwa_index.cwl Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48 |
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kf_alignment_optimized_wf
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![]() Path: tests/basic/data/workflows/basic_example_test.cwl Branch/Commit ID: 3633f105235ddd09510afd3f1a6110b98e46470a |
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AltAnalyze ICGS
AltAnalyze ICGS =============== |
![]() Path: workflows/altanalyze-icgs.cwl Branch/Commit ID: 60854b5d299df91e135e05d02f4be61f6a310fbc |
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count-lines4-wf.cwl
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![]() Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl Branch/Commit ID: 6300a49ec29be956ab451311fe9781522f461aee |
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Generate genome index bowtie
Workflow makes indices for [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016). Executes `bowtie-index` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a directory |
![]() Path: workflows/bowtie-index.cwl Branch/Commit ID: 6bf56698c6fe6e781723dea32bc922b91ef49cf3 |
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wf_trim_and_map_chimeric_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_chimeric_se.cwl Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256 |
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Generate ATDP heatmap using Homer
Generate ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension |
![]() Path: workflows/heatmap.cwl Branch/Commit ID: 6bf56698c6fe6e781723dea32bc922b91ef49cf3 |
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RNA-seq alelle specific pipeline for paired-end data
Allele specific RNA-Seq paired-end workflow |
![]() Path: workflows/allele-rnaseq-pe.cwl Branch/Commit ID: 6bf56698c6fe6e781723dea32bc922b91ef49cf3 |
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count-lines11-extra-step-wf.cwl
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![]() Path: v1.0/v1.0/count-lines11-extra-step-wf.cwl Branch/Commit ID: 1f501e38ff692a408e16b246ac7d64d32f0822c2 |