Explore Workflows

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Graph	Name	Retrieved From	View
	1st-workflow.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/1st-workflow.cwl Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb
	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: b957a4f681bf0ca8ebba4e0d0ec3936bf79620c5
	Nested workflow example	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/nested.cwl Branch/Commit ID: 216fbe57afcf67d81c99b49c1aa3aee0844f0a6a
	mut.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/mut.cwl Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb
	oc-workflow.cwl	https://github.com/karchinlab/opencravat-cwl.git Path: oc-workflow.cwl Branch/Commit ID: d3dd7c649d229d4a0d78c1ba5ccef560da8f09a0
	baysorStaged.cwl	https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git Path: steps/baysorStaged.cwl Branch/Commit ID: 03b8da4ede3afcbf97b4e780c153155f33e76c84
	WGS and MT analysis for fastq files rna / protein - qc, preprocess, filter, annotation, index, abundance	https://github.com/MG-RAST/pipeline.git Path: CWL/Workflows/wgs-fastq.workflow.cwl Branch/Commit ID: 81feefc84ec0faecf1ade718001d5f07610e616e
	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: 9bf0aa495735f8081bb5870cb32fc898b9e6eb22
	assm_assm_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 7319ccfd2108929588bdc266d9df198629dfaa65
	mut3.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/mut3.cwl Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb