Explore Workflows

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Graph	Name	Retrieved From	View
	Downsample and HaplotypeCaller	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/downsample_and_recall.cwl Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
	Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)	https://github.com/ncbi/pgap.git Path: bacterial_annot/wf_bacterial_annot_pass2.cwl Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
	pindel parallel workflow	https://github.com/litd/analysis-workflows.git Path: definitions/subworkflows/pindel.cwl Branch/Commit ID: 336f7d1af649f42543baa6be2594cd872919b5b5
	Bisulfite QC tools	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bisulfite_qc.cwl Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
	allele-process-reference.cwl	https://github.com/datirium/workflows.git Path: subworkflows/allele-process-reference.cwl Branch/Commit ID: 3ceeb2e90f49579369b2e10485908516348381a9
	04-quantification-se-revstranded.cwl RNA-seq 04 quantification	https://github.com/alexbarrera/GGR-cwl.git Path: v1.0/RNA-seq_pipeline/04-quantification-se-revstranded.cwl Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
	grep-and-count-for-figure-1.cwl	https://github.com/manabuishii/cwl-samples.git Path: grep-and-count-for-figure-1.cwl Branch/Commit ID: 752ef34cfa64ba020ef2d70924fb1e8fea889612
	Motif Finding with HOMER with random background regions Motif Finding with HOMER with random 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. Here is how we generate background for Motifs Analysis ------------------------------------- 1. Take input file with regions in a form of “chr\" “start\" “end\" 2. Sort and remove duplicates from this regions file 3. Extend each region in 20Kb into both directions 4. Merge all overlapped extended regions 5. Subtract not extended regions from the extended ones 6. Randomly distribute not extended regions within the regions that we got as a result of the previous step 7. Get fasta file from these randomly distributed regions (from the previous step). Use it as background 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.cwl Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
	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: tools/heatmap-prepare.cwl Branch/Commit ID: 433c10a6ee9f9b07f1af4141e3df6a584dfe86a1
	download_gtf.cwl	https://github.com/yyoshiaki/VIRTUS.git Path: workflow/download_gtf.cwl Branch/Commit ID: 49687daefb8ae715386f722702755ffaa49283e6