Explore Workflows

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

Graph	Name	Retrieved From	View
	Single-cell Differential Expression Single-cell Differential Expression =================================== Runs differential expression analysis for a subset of cells between two selected conditions.	https://github.com/datirium/workflows.git Path: workflows/sc_diff_expr.cwl Branch/Commit ID: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb
	Nested workflow example	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/double-nested.cwl Branch/Commit ID: 12993a6eb60f5ccb4edbe77cb6de661cfc496090
	Cell Ranger Build Reference Indices Cell Ranger Build Reference Indices ===================================	https://github.com/datirium/workflows.git Path: workflows/cellranger-mkref.cwl Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1
	preprocess_vcf.cwl This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.	https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git Path: preprocess_vcf.cwl Branch/Commit ID: 00e98923d9ce49790080f88ae46f3d73a19eb65b
	gcaccess_from_list	https://github.com/ncbi/pgap.git Path: task_types/tt_gcaccess_from_list.cwl Branch/Commit ID: 8cc9b995bca666c54c673a5eb8d9b8c6f8e84490
	Functional analyis of sequences that match the 16S SSU	https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git Path: workflows/16S_taxonomic_analysis.cwl Branch/Commit ID: f914942b9d7bfbabecb872f5945698fcfa09ec80
	811.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/811.cwl Branch/Commit ID: 12993a6eb60f5ccb4edbe77cb6de661cfc496090
	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: 1f03ff02ef829bdb9d582825bcd4ca239e84ca2e
	tt_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: 2353ee2550529ca5b0705c94b32022a21713db18
	exomeseq-gatk4-02-variantdiscovery.cwl	https://github.com/Duke-GCB/bespin-cwl.git Path: subworkflows/exomeseq-gatk4-02-variantdiscovery.cwl Branch/Commit ID: bbe24d8d7fde2e918583b96805909a2867b749d6