Explore Workflows

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Graph Name Retrieved From View
workflow graph Cell Ranger Build V(D)J Reference Indices

Cell Ranger Build V(D)J Reference Indices Build a Cell Ranger V(D)J-compatible reference folder from a user-supplied genome FASTA and gene GTF files.

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

Path: workflows/cellranger-mkvdjref.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
workflow graph trim-chipseq-se.cwl

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/trim-chipseq-se.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
workflow graph methylCtools_index.cwl

https://github.com/ifishlin/Benchmarking_CWL.git

Path: workflows/methylCtools/tools/methylCtools_index.cwl

Branch/Commit ID: 1416ade270d1b990087e39c6680464c12cf564cc
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: 2c7879b47890b9300ab9b5ebd35e17372e077757
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: 252e7214ac64cb1128881e76743013e61bc7ec38
workflow graph Genomic regions intersection and visualization

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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

Path: workflows/intervene.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph count-lines7-wf_v1_1.cwl

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

Path: testdata/count-lines7-wf_v1_1.cwl

Branch/Commit ID: 7af75226f084349e401b1114f25bdcdee060e127
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed 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. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-mitochondrial.cwl

Branch/Commit ID: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726
workflow graph linc_calibrator.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_calibrator.cwl

Branch/Commit ID: 035f66ec0f260628424c9621aed97f7cbf35e737
workflow graph SPRM pipeline

https://github.com/hubmapconsortium/sprm.git

Path: pipeline.cwl

Branch/Commit ID: d2d5127251fbec9f9621df0c6c8c989e3f1b76ba