Explore Workflows

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

Graph	Name	Retrieved From	View
	snaptools_create_snap_file.cwl	https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git Path: steps/snaptools_create_snap_file.cwl Branch/Commit ID: 44dbe381f68878ab607b167b62267c4ea97f3322
	Filter single sample sv vcf from depth callers(cnvkit/cnvnator)	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sv_depth_caller_filter.cwl Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
	Filter ChIP/ATAC/cut&run/diffbind peaks for Tag Density Profile or Motif Enrichment analyses Filters ChIP/ATAC/cut&run/diffbind peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC/cut&run/diffbind pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.	https://github.com/datirium/workflows.git Path: workflows/filter-peaks-for-heatmap.cwl Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
	Subworkflow that runs cnvkit in single sample mode and returns a vcf file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
	Restore contig names Restore the contig names using the map file in ppmeta, virfinder and virsorter output files.	https://github.com/EBI-Metagenomics/emg-viral-pipeline.git Path: cwl/src/Tools/RestoreOutputNames/restore_tools_outputs_swf.cwl Branch/Commit ID: b0ed3f07c8faced85609287759596ad83e154977
	Filter single sample sv vcf from paired read callers(Manta/Smoove)	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
	stdout-wf_v1_0.cwl	https://github.com/common-workflow-language/cwl-utils.git Path: testdata/stdout-wf_v1_0.cwl Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
	fasta2taxa-plot Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.	https://github.com/MG-RAST/qiime-pipeline.git Path: CWL/Workflows/qiime/join-reads2plot.cwl Branch/Commit ID: 3565f6f4d26f5709aff56e6a266dbb7c7d6129d8
	IMG/VR blast Run blast against IMG/VR	https://github.com/EBI-Metagenomics/emg-viral-pipeline.git Path: cwl/src/Tools/IMGvrBlast/imgvr_blast_swf.cwl Branch/Commit ID: b0ed3f07c8faced85609287759596ad83e154977
	Deprecated. 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 markdup` samtools\_remove\_duplicates to get rid of duplicated reads. 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: fa4f172486288a1a9d23864f1d6962d85a453e16