Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines11-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b
workflow graph Xenbase RNA-Seq pipeline paired-end

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-pe.cwl

Branch/Commit ID: 7518b100d8cbc80c8be32e9e939dfbb27d6b4361
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: ae75b938e6e8ae777a55686bbacad824b3c6788c
workflow graph extract_amplicon_kit.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_amplicon_kit.cwl

Branch/Commit ID: 17823fcd036d134df803fbf76e23b0bc5eabedfd
workflow graph star_samtools_miso.cwl

https://github.com/rawgene/cwl.git

Path: workflows/star_samtools_miso.cwl

Branch/Commit ID: ff0e5dfe44fb85900b5563ab340de8ad3d952eb5
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: be32f1363f9a9a9247d738e9593b207e9c5172c8
workflow graph workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_download/workflow.cwl

Branch/Commit ID: 57ccb57b0b84aafd91bdfec0b02f814227de4ad5
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: 8cc9b995bca666c54c673a5eb8d9b8c6f8e84490
workflow graph scatter-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl

Branch/Commit ID: 0db44e3c9805a070564f954222efff71cd791b70
workflow graph cwlsite.cwl

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

Path: cwltool/schemas/site/cwlsite.cwl

Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534