Explore Workflows

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

Graph Name Retrieved From View
workflow graph sum-wf.cwl

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

Path: tests/sum-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph step-valuefrom4-wf.cwl

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

Path: tests/step-valuefrom4-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph count-lines15-wf.cwl

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

Path: tests/count-lines15-wf.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph kfdrc_qc_wf.cwl

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

Path: workflows/kfdrc_qc_wf.cwl

Branch/Commit ID: af97e25cb213233a4923c881f7c6210b57960cb9
workflow graph RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

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

Path: workflows/rnaseq-se-dutp.cwl

Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058
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: 49508a2757ff2f49f1c200774a38af1c12b531bf
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9
workflow graph step-valuefrom2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl

Branch/Commit ID: 6e9f82a6d2195d4f16f28fd6e1485138372fb430
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735
workflow graph search.cwl#main

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

Path: tests/search.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

Packed ID: main