Explore Workflows

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

Graph Name Retrieved From View
workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: 789267ce0e3fed674ea5212a562315218fcf1bfc
workflow graph record-output-wf_v1_1.cwl

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

Path: testdata/record-output-wf_v1_1.cwl

Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51
workflow graph cond-wf-013.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-013.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph scatter-wf3.cwl#main

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

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

Branch/Commit ID: 526f36f93655bfb098f766ff020708b5a707513a

Packed ID: main
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 49508a2757ff2f49f1c200774a38af1c12b531bf
workflow graph Single-Cell Preprocessing Cell Ranger Pipeline

Devel version of Single-Cell Preprocessing Cell Ranger Pipeline ===============================================================

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: e99e80a2c19682d59947bde04a892d7b6d90091c
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: 49508a2757ff2f49f1c200774a38af1c12b531bf
workflow graph conflict-wf.cwl#collision

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

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

Branch/Commit ID: fd6e054510e2bb65eed4069a3a88013d7ecbb99c

Packed ID: collision
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: a93be3183c2218ee50f13ae2675dd1cde563fdbc
workflow graph CLIP-Seq pipeline for single-read experiment NNNNG

Cross-Linking ImmunoPrecipitation ================================= `CLIP` (`cross-linking immunoprecipitation`) is a method used in molecular biology that combines UV cross-linking with immunoprecipitation in order to analyse protein interactions with RNA or to precisely locate RNA modifications (e.g. m6A). (Uhl|Houwaart|Corrado|Wright|Backofen|2017)(Ule|Jensen|Ruggiu|Mele|2003)(Sugimoto|König|Hussain|Zupan|2012)(Zhang|Darnell|2011) (Ke| Alemu| Mertens| Gantman|2015) CLIP-based techniques can be used to map RNA binding protein binding sites or RNA modification sites (Ke| Alemu| Mertens| Gantman|2015)(Ke| Pandya-Jones| Saito| Fak|2017) of interest on a genome-wide scale, thereby increasing the understanding of post-transcriptional regulatory networks. The identification of sites where RNA-binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV cross-linking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from _in vivo_ cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high-throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide maps of RNA binding with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. The application of CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of cross-link–induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes ~8 d to prepare RNA for sequencing. Established pipelines for data analysis, including those for CIMS, take 3–4 d. Workflow -------- CLIP begins with the in-vivo cross-linking of RNA-protein complexes using ultraviolet light (UV). Upon UV exposure, covalent bonds are formed between proteins and nucleic acids that are in close proximity. (Darnell|2012) The cross-linked cells are then lysed, and the protein of interest is isolated via immunoprecipitation. In order to allow for sequence specific priming of reverse transcription, RNA adapters are ligated to the 3' ends, while radiolabeled phosphates are transferred to the 5' ends of the RNA fragments. The RNA-protein complexes are then separated from free RNA using gel electrophoresis and membrane transfer. Proteinase K digestion is then performed in order to remove protein from the RNA-protein complexes. This step leaves a peptide at the cross-link site, allowing for the identification of the cross-linked nucleotide. (König| McGlincy| Ule|2012) After ligating RNA linkers to the RNA 5' ends, cDNA is synthesized via RT-PCR. High-throughput sequencing is then used to generate reads containing distinct barcodes that identify the last cDNA nucleotide. Interaction sites can be identified by mapping the reads back to the transcriptome.

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

Path: workflows/clipseq-se.cwl

Branch/Commit ID: e99e80a2c19682d59947bde04a892d7b6d90091c