Explore Workflows

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

Graph Name Retrieved From View
workflow graph assemble.cwl

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: 77a9fa25b89ce73582a1ce6ba75fa6d2537fb8e8
workflow graph Xenbase ChIP-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 (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-pe.cwl

Branch/Commit ID: 9ee330737f4603e4e959ffe786fbb2046db70a00
workflow graph no-inputs-wf.cwl

Workflow without inputs.

 https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/no-inputs-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph count-lines13-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines13-wf.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 72c3091012f5c2dce38ad9213cda617d2c7a61ac
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: 3ee63d8757c341ca98b3b46ec4782862ad19b710
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_nonhuman.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph js-expr-req-wf.cwl#wf

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: ae401a813472ca453a99ad067a5e6fc3bd71112b

Packed ID: wf
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: 0a9a4ce83b49ed4e7eee5bcc09d83725136a36b0