Explore Workflows

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

Graph Name Retrieved From View
workflow graph 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 **strand specific single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. 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/rnaseq-se-dutp.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph Single-cell RNA-Seq Cluster Analysis

Single-cell RNA-Seq Cluster Analysis Clusters single-cell RNA-Seq datasets, identifies gene markers.

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

Path: workflows/sc-rna-cluster.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph Motif Finding with HOMER from FASTA files

Motif Finding with HOMER from FASTA files --------------------------------------------------- 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.cwl

Branch/Commit ID: ee66d03be8a7fd61367db40c37a973ff55ece4da
workflow graph trim-chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-chipseq-pe.cwl

Branch/Commit ID: 801f7b363e0599b9a28ecda696dfdb1c0e40ce71
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5
workflow graph indexing_bed

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/indexing_bed.cwl

Branch/Commit ID: 548778e1733b1cac01ed2ec3d25a14bc484f3cbd
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: 1b8d71c75156a1a62bf0477d59db26010e2dcc29
workflow graph 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: 57863b6131d8262c5ce864adaf8e4038401e71a2
workflow graph gather AML trio outputs

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

Path: definitions/pipelines/aml_trio_cle_gathered.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6