Explore Workflows

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

Graph Name Retrieved From View
workflow graph steplevel-resreq.cwl

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

Path: cwltool/schemas/v1.0/v1.0/steplevel-resreq.cwl

Branch/Commit ID: 0e98de8f692bb7b9626ed44af835051750ac20cd
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: 6003cbb94f16103241b562f2133e7c4acac6c621
workflow graph Cellranger Reanalyze

Cellranger Reanalyze

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph nestedworkflows.cwl

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

Path: cwltool/schemas/v1.0/examples/nestedworkflows.cwl

Branch/Commit ID: d7481d03fa4b5b4630392540f598acfb100b421d
workflow graph amplicon-wf--v.5-cond.cwl

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/amplicon-wf--v.5-cond.cwl

Branch/Commit ID: 4b98d8bf882bc96d924b5d2d4e6d9c188fa7b273
workflow graph Cell Ranger Count Gene Expression

Cell Ranger Count Gene Expression Quantifies gene expression from a single-cell RNA-Seq library.

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

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

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph kfdrc_rgbam_to_realnbam.cwl

https://github.com/inab/kf-alignment-workflow.git

Path: subworkflows/kfdrc_rgbam_to_realnbam.cwl

Branch/Commit ID: 425c6561b6c52139190666b761cb0350cfd8ad9c
workflow graph star_samtools_stringtie-prepDE-DESeq2.htseq-dexseq.cwl

https://github.com/rawgene/cwl.git

Path: workflows/star_samtools_stringtie-prepDE-DESeq2.htseq-dexseq.cwl

Branch/Commit ID: 33a3cdba1184ad14e7a168eef3c505b9b4332f47
workflow graph Single-cell Pseudobulk Differential Expression Analysis Between Datasets

Single-cell Pseudobulk Differential Expression Analysis Between Datasets Identifies differentially expressed genes between groups of cells coerced to pseudobulk datasets.

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

Path: workflows/sc-rna-de-pseudobulk.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph RNA-Seq pipeline single-read strand specific

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 **strand specific single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. 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/rnaseq-se-dutp.cwl

Branch/Commit ID: 42dc4f70b117e78785b82865ec4c4b941ac1c259