Explore Workflows

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

Path: tests/wf/nested.cwl

Branch/Commit ID: 047e69bb169e79fad6a7285ee798c4ecec3b218b

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de

Packed ID: wf

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 1ce371c7412debef75edf09e8830d74ac987a668

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

Path: definitions/pipelines/somatic_exome_gathered.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: ac387721a55fd91df3dcdf16e199354618b136d1

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

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a

Differential Binding Analysis of ChIP-Seq or CUT&RUN/Tag Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq or CUT&RUN/Tag data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by peak caller tools and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP or CUT&RUN/Tag experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4.

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

Path: workflows/diffbind.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: ddc35c559d1ac6aab4972fe1a2b63300c4373f54

ChIP-seq 03 mapping - reads: PE

https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/03-map-pe.cwl

Branch/Commit ID: c50b80e9b0eaaf4613f9feca44b3463bbfd288d5

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: 5561f7ee11dd74848680351411a19aa87b13d27b