Explore Workflows

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

Graph Name Retrieved From View
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
workflow graph spurious_annot

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: aa64bf6a90e0780ab564de865dbb027df98c0a01
workflow graph Build Bowtie indices

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome

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

Path: workflows/bowtie-index.cwl

Branch/Commit ID: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d
workflow graph Add snv and indel bam-readcount files to a vcf

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

Path: definitions/subworkflows/vcf_readcount_annotator.cwl

Branch/Commit ID: 449bc7e45bb02316d040f73838ef18359e770268
workflow graph Hello World

Puts a message into a file using echo

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

Path: src/test/resources/cwl/hello/hello.cwl

Branch/Commit ID: d522c1e2e1f2595bb584a131b08ff660d05650ab

Packed ID: main
workflow graph Filter Protein Seeds I; Find ProSplign Alignments I

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: 546742b523ce12f6246a52c838a51920a08dad4b
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_dispatch/2other_species/workflow.cwl

Branch/Commit ID: 22c18af26fa088b2b31ebb27d38a7e81d21b6d08
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: d6f58c383d0676269afb519399061191a1144a6a
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_apollo2_data_processing/processing/workflow.cwl

Branch/Commit ID: 337527c5512d2fb7644814bbfb4a338fd45ec907
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_dispatch/2blat/workflow.cwl

Branch/Commit ID: 22c18af26fa088b2b31ebb27d38a7e81d21b6d08