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Graph	Name	Retrieved From	View
	Cellranger reanalyze - reruns secondary analysis performed on the feature-barcode matrix Devel version of Single-Cell Cell Ranger Reanalyze ================================================== Workflow calls \"cellranger aggr\" command to rerun secondary analysis performed on the feature-barcode matrix (dimensionality reduction, clustering and visualization) using different parameter settings. As an input we use filtered feature-barcode matrices in HDF5 format from cellranger count or aggr experiments. Note, we don't pass aggregation_metadata from the upstream cellranger aggr step. Need to address this issue when needed.	https://github.com/datirium/workflows.git Path: workflows/cellranger-reanalyze.cwl Branch/Commit ID: 64f7fe4438898218fd83133efa25251078f5b27e
	default-dir5.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/default-dir5.cwl Branch/Commit ID: 819c81af5449ec912bbbbead042ad66b8d3fd8d4
	wgs alignment with qc	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/wgs_alignment.cwl Branch/Commit ID: 1437aed13d240fd624f78df2c7efb096c5079d73
	align_merge_sas	https://github.com/ncbi/pgap.git Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: 3e7a3c1cc1ed5164ae0a51a96f20d7c480d1d70b
	Cell Ranger Build Reference Indices Cell Ranger Build Reference Indices ===================================	https://github.com/datirium/workflows.git Path: workflows/cellranger-mkref.cwl Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d
	ani_top_n	https://github.com/ncbi/pgap.git Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: 23f0ee7a36649ab37cabdd9277b7c82d098be79c
	Single-Cell RNA-Seq Cluster Analysis Single-Cell RNA-Seq Cluster Analysis Clusters cells by similarity of gene expression data from the outputs of the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” pipeline. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, and “Single-Cell Differential Abundance Analysis” pipelines.	https://github.com/datirium/workflows.git Path: workflows/sc-rna-cluster.cwl Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e
	gathered exome alignment and somatic variant detection for cle purpose	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome_cle_gathered.cwl Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
	tt_hmmsearch_wnode.cwl	https://github.com/ncbi/pgap.git Path: task_types/tt_hmmsearch_wnode.cwl Branch/Commit ID: f403d9e26d60d3e3591a03077bc9dfa188b1c2bb
	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: 64f7fe4438898218fd83133efa25251078f5b27e