Explore Workflows

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

Graph Name Retrieved From View
workflow graph Cellranger reanalyze - reruns secondary analysis performed on the feature-barcode matrix

Devel version of Single-Cell Cell Ranger Reanalyze ================================================== Workflow calls \"cellranger aggr\" command to rerun secondary analysis performed on the feature-barcode matrix (dimensionality reduction, clustering and visualization) using different parameter settings. As an input we use filtered feature-barcode matrices in HDF5 format from cellranger count or aggr experiments. Note, we don't pass aggregation_metadata from the upstream cellranger aggr step. Need to address this issue when needed.

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422
workflow graph mut.cwl

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

Path: tests/wf/mut.cwl

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs_gvcf.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086
workflow graph Bisulfite alignment and QC

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f
workflow graph chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

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

Path: workflows/chipseq-pe.cwl

Branch/Commit ID: bc75349ad3a7bdce82b4cd8584501f4d0280bb8d
workflow graph scatter-valuefrom-wf1.cwl

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

Path: tests/scatter-valuefrom-wf1.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph gathered exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_gathered.cwl

Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb
workflow graph Trim Galore 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 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-dutp.cwl

Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422
workflow graph basename-fields-test.cwl

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

Path: cwltool/schemas/v1.0/v1.0/basename-fields-test.cwl

Branch/Commit ID: 62ae25772a8e98b6591554882daa3f3758079fca
workflow graph sec-wf.cwl

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

Path: tests/wf/sec-wf.cwl

Branch/Commit ID: e62a8406b448220969ee172699f61c5ca379d60c