Explore Workflows

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

Graph Name Retrieved From View
workflow graph RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl

Branch/Commit ID: 564156a9e1cc7c3679a926c479ba3ae133b1bfd4
workflow graph gather AML trio outputs

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

Path: definitions/pipelines/aml_trio_cle_gathered.cwl

Branch/Commit ID: 40097e1ed094c5b42b68f3db2ff2cbe78c182479
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
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