Explore Workflows

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

Graph Name Retrieved From View
workflow graph Cell Ranger ARC Count Gene Expression + ATAC

Cell Ranger ARC Count Gene Expression + ATAC ============================================

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

Path: workflows/cellranger-arc-count.cwl

Branch/Commit ID: c0ca7b140d776eec223ceb1c620eda17281860c4
workflow graph chipseq-gen-bigwig.cwl

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

Path: subworkflows/chipseq-gen-bigwig.cwl

Branch/Commit ID: 7518b100d8cbc80c8be32e9e939dfbb27d6b4361
workflow graph schemadef-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59
workflow graph Trim Galore RNA-Seq pipeline single-read

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.cwl

Branch/Commit ID: b5e16e359007150647b14dc6e038f4eb8dccda79
workflow graph ani.cwl

Perform taxonomic identification tasks on an input genome

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

Path: ani.cwl

Branch/Commit ID: b560e3abadfb150a0013376d7a189df066ab56f9
workflow graph Chipseq alignment for nonhuman with qc and creating homer tag directory

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/chipseq_alignment_nonhuman.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph any-type-compat.cwl

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

Path: cwltool/schemas/v1.0/v1.0/any-type-compat.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a
workflow graph gwas.cwl

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/gwas.cwl

Branch/Commit ID: ed0ce8d076784685a2e49173241b63e427d7a320
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 0d0ba0c3410e8aee55c82f077cee31d8ee929b5a
workflow graph Filter ChIP/ATAC peaks for Tag Density Profile or Motif Enrichment analyses

Filters ChIP/ATAC peaks with the neatest genes assigned for Tag Density Profile or Motif Enrichment analyses ============================================================================================================ Tool filters output from any ChIP/ATAC pipeline to create a file with regions of interest for Tag Density Profile or Motif Enrichment analyses. Peaks with duplicated coordinates are discarded.

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

Path: workflows/filter-peaks-for-heatmap.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf