Explore Workflows

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

Graph Name Retrieved From View
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: d6ec0dee61ef65a110e10141bde1a79332a64ab0
workflow graph count-lines6-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: ae75b938e6e8ae777a55686bbacad824b3c6788c
workflow graph PGAP Pipeline, simple user input, PGAPX-134

PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)

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

Path: pgap.cwl

Branch/Commit ID: 4ea5956bb97ea2eb6de124bc9b6a6a81a14fd2e7
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/wgs_alignment.cwl

Branch/Commit ID: ec5355f335852e51c6938809c16ea1d230a3f983
workflow graph transform.cwl

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

Path: workflows/fastq_readgroup_stats/transform.cwl

Branch/Commit ID: 17823fcd036d134df803fbf76e23b0bc5eabedfd
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 195b4ab487c939eb32a55d9f78bc1befd100caae
workflow graph extract_readgroup_fastq_pe_http.cwl

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

Path: workflows/bamfastq_align/extract_readgroup_fastq_pe_http.cwl

Branch/Commit ID: 18affdd927cc388fab2c113dc2ec6df782af2a52
workflow graph env-wf3.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: 4c905b830371eee45188a53510ba0ee9113fd4c8
workflow graph kfdrc_bwamem_subwf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/dev/ultra-opt/kfdrc_bwamem_subwf.cwl

Branch/Commit ID: dbaad281888ab5346892917c11ea3dd61ce2fbbd