Explore Workflows

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

Graph Name Retrieved From View
workflow graph 04-quantification-pe-revstranded.cwl

RNA-seq 04 quantification

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

Path: v1.0/RNA-seq_pipeline/04-quantification-pe-revstranded.cwl

Branch/Commit ID: 7696e7eb27a9251fba53ef4ccacc84cc8f8b0685
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: ec5355f335852e51c6938809c16ea1d230a3f983
workflow graph PGAP Pipeline

PGAP pipeline for external usage, powered via containers

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

Path: wf_common.cwl

Branch/Commit ID: 7e3e1cb249e85285e27ef3ebd4104965f835241d
workflow graph download_root.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/unix/download_root.cwl

Branch/Commit ID: 18affdd927cc388fab2c113dc2ec6df782af2a52
workflow graph Xenbase ChIP-Seq pipeline single-read

1. Convert input SRA file into FASTQ file (run fastq-dump) 2. Analyze quality of FASTQ file (run fastqc) 3. If any of the following fields in fastqc generated report is marked as failed: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ file to reference genome (run Bowtie2) 5. Sort and index generated by Bowtie2 BAM file (run samtools sort, samtools index) 6. Remove duplicates in sorted BAM file (run picard) 7. Sort and index BAM file after duplicates removing (run samtools sort, samtools index) 8. Count mapped reads number in sorted BAM file (run bamtools stats) 9. Generate genome coverage BED file (run bedtools genomecov) 10. Sort genearted BED file (run sort) 11. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-chipseq-se.cwl

Branch/Commit ID: 7518b100d8cbc80c8be32e9e939dfbb27d6b4361
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 7e3e1cb249e85285e27ef3ebd4104965f835241d
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5
workflow graph transform.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/dnaseq/validate/transform.cwl

Branch/Commit ID: 18affdd927cc388fab2c113dc2ec6df782af2a52
workflow graph unix_align_workflow.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/unix/unix_align_workflow.cwl

Branch/Commit ID: 18affdd927cc388fab2c113dc2ec6df782af2a52
workflow graph iwdr_with_nested_dirs.cwl

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

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534