Explore Workflows

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

Graph	Name	Retrieved From	View
	Bisulfite alignment and QC	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/bisulfite.cwl Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c
	count-lines13-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c
	idr.cwl	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/ChIP-Seq/idr.cwl Branch/Commit ID: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
	trim-rnaseq-pe-dutp.cwl Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.	https://github.com/datirium/workflows.git Path: workflows/trim-rnaseq-pe-dutp.cwl Branch/Commit ID: cb5e5b8563be4977e9f2babc14fe084faa234847
	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: 4642316a30a95d4f3d135c18f98477886b160094 Packed ID: wf
	Immunotherapy Workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/immuno.cwl Branch/Commit ID: 449bc7e45bb02316d040f73838ef18359e770268
	output_reference_workflow_input.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/output_reference_workflow_input.cwl Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf
	format_rrnas_from_seq_entry	https://github.com/ncbi/pgap.git Path: task_types/tt_format_rrnas_from_seq_entry.cwl Branch/Commit ID: f18c1dce463509170ee3bf2844d5a3637ff706f5
	Whole genome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_wgs.cwl Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
	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: 7eef0294395d83ff0765fce61726a59d71126422