Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 4ab9399a4777610a579ea2c259b9356f27641dcc
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 3a287b7cb6162cdea79865235d224fea45963d87
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: 3a287b7cb6162cdea79865235d224fea45963d87
workflow graph split-bams-by-strand-and-index.cwl

Split reads in a BAM file by strands and index forward and reverse output BAM files

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/quant/split-bams-by-strand-and-index.cwl

Branch/Commit ID: 4e568335133405d28f4b73ae11e7f51f2900dfa3
workflow graph split-bams-by-strand-and-index.cwl

Split reads in a BAM file by strands and index forward and reverse output BAM files

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/quant/split-bams-by-strand-and-index.cwl

Branch/Commit ID: 6e008c1170ef818b6c4c63f0eec7baa4f7be7b3c
workflow graph 02-trim-pe.cwl

ChIP-seq 02 trimming - reads: PE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: 8d02684ae0ff27e641f3704686e3bc8b1979b854
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 0b6e8fd8ead7644cf5398395b76af5cf4011686f
workflow graph 02-peakcall.cwl

DNase-seq 02 quantification

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/DNase-seq_pipeline/02-peakcall.cwl

Branch/Commit ID: 4e568335133405d28f4b73ae11e7f51f2900dfa3
workflow graph mug_refinement.cwl

https://github.com/bioexcel/virtualscreening.git

Path: cwl/mug_refinement.cwl

Branch/Commit ID: e973958e012e38f99b0c8ed2b798c5e5a7f72b22
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 3a287b7cb6162cdea79865235d224fea45963d87