Explore Workflows

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

Graph Name Retrieved From View
workflow graph Gathered Downsample and HaplotypeCaller

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

Path: definitions/pipelines/gathered_downsample_and_recall.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph 03-map-se.cwl

ChIP-seq 03 mapping - reads: SE

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

Path: v1.0/ChIP-seq_pipeline/03-map-se.cwl

Branch/Commit ID: 33385c6a820a9d4d18cff6fc3a533ec8e3c11c6e
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: 5677d6df78453e62d2e78ab485f216feaef91681
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 5677d6df78453e62d2e78ab485f216feaef91681
workflow graph count-lines11-wf-noET.cwl

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

Path: v1.0/v1.0/count-lines11-wf-noET.cwl

Branch/Commit ID: 9a23706ec061c5d2c02ff60238d218aadf0b5db9
workflow graph wgs alignment and tumor-only variant detection

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

Path: definitions/pipelines/wgs.cwl

Branch/Commit ID: 1560e7817fdb71d58aca7f98aba68809d840ade1
workflow graph Generate genome indices for Bismark

Copy genome_fasta 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_fasta file basename without extension.

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

Path: workflows/bismark-indices.cwl

Branch/Commit ID: e238d1756f1db35571e84d72e1699e5d1540f10c
workflow graph Cut-n-Run pipeline paired-end

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: aebf2355539fdf81fd9082616f8b21440d2691c6
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: 5677d6df78453e62d2e78ab485f216feaef91681
workflow graph Xenbase RNA-Seq pipeline single-read

1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump) 2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files) 3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ files to reference genome, calculate genes and isoforms expression (run RSEM) 5. Count mapped reads number in sorted BAM file (run bamtools stats) 6. Generate genome coverage BED file (run bedtools genomecov) 7. Sort genearted BED file (run sort) 8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-rnaseq-se.cwl

Branch/Commit ID: e238d1756f1db35571e84d72e1699e5d1540f10c