Explore Workflows

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

Graph Name Retrieved From View
workflow graph default-dir5.cwl

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

Path: tests/wf/default-dir5.cwl

Branch/Commit ID: e62a8406b448220969ee172699f61c5ca379d60c
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 25aa4788dd4efb1cc8ed6f609cb7803896e4d28d
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed 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. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-mitochondrial.cwl

Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3
workflow graph Bisulfite alignment and QC

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: 195b4ab487c939eb32a55d9f78bc1befd100caae
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 68b828ac482956a03325623d817780986f34fb31
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: ffab5424bb8b5905aecf6f8e2e6387da7f3df562
workflow graph 1st-workflow.cwl

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c
workflow graph kmer_top_n

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 251343ee5b7586ba2cf89458555f1da87a7558f2
workflow graph kfdrc_sentieon_gvcf_wf.cwl

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

Path: workflows/kfdrc_sentieon_gvcf_wf.cwl

Branch/Commit ID: a7e45d17fb56ead5a4c65628689915316341fbde
workflow graph bulk_analysis.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_analysis.cwl

Branch/Commit ID: d0e845df600fff7944943e2520db7a0cda8d00db