Explore Workflows

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40

Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe-dutp.cwl

Branch/Commit ID: 46a077b51619c6a14f85e0aa5260ae8a04426fab

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: 12e5256de1b680c551c87fd5db6f3bc65428af67

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c

Packed ID: main

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5

Single-cell RNA-Seq Filtering Analysis Filters single-cell RNA-Seq datasets based on the common QC metrics.

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

Path: workflows/sc-rna-filter.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: b4a6e46405c08e0b14ad92f0ab38bcc4a69caa5c

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: f403d9e26d60d3e3591a03077bc9dfa188b1c2bb