Explore Workflows

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Graph Name Retrieved From View
workflow graph count-lines11-wf-noET.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines11-wf-noET.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3
workflow graph Motif Finding with HOMER with custom background regions

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

 https://github.com/datirium/workflows.git

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph foreign_screening.cwl

https://github.com/ncbi/pgap.git

Path: vecscreen/foreign_screening.cwl

Branch/Commit ID: 5b498b4c4f17bb8f17e6886aa4c5661d7aba34fc
workflow graph Build Bowtie indices

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome

 https://github.com/datirium/workflows.git

Path: workflows/bowtie-index.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/datirium/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph Single-Cell ATAC-Seq Dimensionality Reduction Analysis

Single-Cell ATAC-Seq Dimensionality Reduction Analysis Removes noise and confounding sources of variation by reducing dimensionality of chromatin accessibility data from the outputs of “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipelines. The results of this workflow are primarily used in “Single-Cell ATAC-Seq Cluster Analysis” or “Single-Cell WNN Cluster Analysis” pipelines.

 https://github.com/datirium/workflows.git

Path: workflows/sc-atac-reduce.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph umi per-lane alignment subworkflow

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: ddb49a0951d9ad537269d7db3fe8f904495a8bf4
workflow graph Single-cell Format Transform

Single-cell Format Transform Transforms single-cell sequencing data formats into Cell Ranger like output.

https://github.com/datirium/workflows.git

Path: workflows/sc-format-transform.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph Trim Galore RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

 https://github.com/datirium/workflows.git

Path: workflows/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: b957a4f681bf0ca8ebba4e0d0ec3936bf79620c5
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/datirium/workflows.git

Path: subworkflows/heatmap-prepare.cwl

Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf