Explore Workflows

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

Graph	Name	Retrieved From	View
	Detect DoCM variants	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/docm_germline.cwl Branch/Commit ID: 31a179d7a2f2ac86bfd7fcc4dc79832c3739ae76
	count-lines11-wf.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/count-lines11-wf.cwl Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
	ChIP-Seq pipeline paired-end The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) ChIP-Seq basic analysis workflow for a paired-end experiment. A [FASTQ](http://maq.sourceforge.net/fastq.shtml) input file has to be provided. The pipeline produces a sorted BAM file alongside with index BAI file, quality statistics of the input FASTQ file, coverage by estimated fragments as a BigWig file, peaks calling data in a form of narrowPeak or broadPeak files, islands with the assigned nearest genes and region type, data for average tag density plot. Workflow starts with step fastx\_quality\_stats from FASTX-Toolkit to calculate quality statistics for input FASTQ file. At the same time `bowtie` is used to align reads from input FASTQ file to reference genome bowtie\_aligner. The output of this step is an unsorted SAM file which is being sorted and indexed by `samtools sort` and `samtools index` samtools\_sort\_index. Depending on workflow’s input parameters indexed and sorted BAM file can be processed by `samtools rmdup` samtools\_rmdup to get rid of duplicated reads. If removing duplicates is not required the original BAM and BAI files are returned. Otherwise step samtools\_sort\_index\_after\_rmdup repeat `samtools sort` and `samtools index` with BAM and BAI files without duplicates. Next `macs2 callpeak` performs peak calling macs2\_callpeak and the next step reports macs2\_island\_count the number of islands and estimated fragment size. If the latter is less that 80bp (hardcoded in the workflow) `macs2 callpeak` is rerun again with forced fixed fragment size value (macs2\_callpeak\_forced). It is also possible to force MACS2 to use pre set fragment size in the first place. Next step (macs2\_stat) is used to define which of the islands and estimated fragment size should be used in workflow output: either from macs2\_island\_count step or from macs2\_island\_count\_forced step. If input trigger of this step is set to True it means that macs2\_callpeak\_forced step was run and it returned different from macs2\_callpeak step results, so macs2\_stat step should return [fragments\_new, fragments\_old, islands\_new], if trigger is False the step returns [fragments\_old, fragments\_old, islands\_old], where sufix \"old\" defines results obtained from macs2\_island\_count step and sufix \"new\" - from macs2\_island\_count\_forced step. The following two steps (bamtools\_stats and bam\_to\_bigwig) are used to calculate coverage from BAM file and save it in BigWig format. For that purpose bamtools stats returns the number of mapped reads which is then used as scaling factor by bedtools genomecov when it performs coverage calculation and saves it as a BEDgraph file whichis then sorted and converted to BigWig format by bedGraphToBigWig tool from UCSC utilities. Step get\_stat is used to return a text file with statistics in a form of [TOTAL, ALIGNED, SUPRESSED, USED] reads count. Step island\_intersect assigns nearest genes and regions to the islands obtained from macs2\_callpeak\_forced. Step average\_tag\_density is used to calculate data for average tag density plot from the BAM file.	https://github.com/datirium/workflows.git Path: workflows/chipseq-pe.cwl Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058
	kmer_top_n_extract	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_top_n_extract.cwl Branch/Commit ID: 2d851682ba1bf2aaaacb3677253b55ceb59c8568
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe
	default-dir5.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/default-dir5.cwl Branch/Commit ID: 9cda157cb4380e9d30dec29f0452c56d0c10d064
	trim-rnaseq-pe.cwl Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.	https://github.com/Barski-lab/workflows.git Path: workflows/trim-rnaseq-pe.cwl Branch/Commit ID: 568da91bb1c6182ba4f146e2a729cac1c3d8783c
	plant2human workflow Novel gene discovery workflow by comparing plant species and model organisms with humans based on structural similarity search.	https://github.com/yonesora56/plant2human.git Path: Workflow/plant2human_v1_1.cwl Branch/Commit ID: 9bd80581d7ced3ee307b020eb4b091e411c3cbfb
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
	bam_readcount workflow	https://github.com/tmooney/cancer-genomics-workflow.git Path: definitions/subworkflows/bam_readcount.cwl Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985