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Graph Name Retrieved From View
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: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph step-valuefrom3-wf_v1_1.cwl

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

Path: testdata/step-valuefrom3-wf_v1_1.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e
workflow graph io-int-default-tool-and-wf.cwl

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

Path: tests/io-int-default-tool-and-wf.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf
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/Barski-lab/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 64e85970dbecba89c3380ab285c108d221e76fe6
workflow graph xenbase-sra-to-fastq-se.cwl

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

Path: workflows/xenbase-sra-to-fastq-se.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e
workflow graph trim-chipseq-se.cwl

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/trim-chipseq-se.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e
workflow graph protein similarities

run diamond on mutlple DBs and merge-sort results

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-diamond.workflow.cwl

Branch/Commit ID: 1844de830f6935901849ccd9966685fbf13e8042
workflow graph Trim Galore RNA-Seq pipeline single-read

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.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: 9c0b1497c467393e1a54735575043dced73e95c4