Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-wf1.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-wf1.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph scatter-wf4.cwl#main

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

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

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3

Packed ID: main
workflow graph extract_file_with_index.cwl

https://github.com/NCI-GDC/aliquot-maf-cwl.git

Path: vcf-to-aliquot-maf/subworkflows/extract_file_with_index.cwl

Branch/Commit ID: 4c0c8a2a75634d4558904678644f1d2f0f0345e8
workflow graph amplicon_metrics.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/amplicon_metrics.cwl

Branch/Commit ID: 20a901f44c9fb0e6f4ee3c40ec33fa4b1c8ef005
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 5c40c5a0464c84076e0e407a0e05522b43bdc0a6
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 5e92165ac2c11608ab2db42fe2d66eabe72dbb40
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html 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-smarter-dutp.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 6a55118f915e24d2ad008c93a02d9de5643f5511
workflow graph xenbase-sra-to-fastq-pe.cwl

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

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: 01c6af7a598eb44f6bcaa9b5eecf13229f28546e