Explore Workflows

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

Graph Name Retrieved From View
workflow graph wf_split_self_and_idr.cwl

This workflow returns the reproducible number of split peaks given a single bam file and its size-matched input pair. This workflow splits the bam file first, but does not do anything to the input.

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_split_self_and_idr.cwl

Branch/Commit ID: 55f4f4f9c10a09ce03c5c531dd176e6080118977
workflow graph Generate genome indices for Bismark

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 folder name.

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

Path: workflows/bismark-indices.cwl

Branch/Commit ID: 2b8146f76595f0c4d8bf692de78b21280162b1d0
workflow graph allele-process-reference.cwl

https://github.com/Barski-lab/workflows.git

Path: subworkflows/allele-process-reference.cwl

Branch/Commit ID: f2aee86fecd321efc6857b124350f079238ea2ba
workflow graph workflow_input_format_expr_v1_1.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/workflow_input_format_expr_v1_1.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28
workflow graph kmer_seq_entry_extract_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
workflow graph 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: workflows/allele-vcf-alignreads-se-pe.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph FASTQ Download

FASTQ Download Assists in downloading problematic single-cell sequencing data from Sequence Read Archive (SRA)

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

Path: workflows/fastq-download.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph advanced-header.cwl

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

Path: metadata/advanced-header.cwl

Branch/Commit ID: d7e214cefcfdabbe6b99d6d3d221998e0dc40e26