Explore Workflows

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

Graph Name Retrieved From View
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph running cellranger mkfastq and count

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph align_merge_sas

https://github.com/ncbi/pgap.git

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 66b5bc323dcd23e1b2c14bf4783babf0f15ca43b
workflow graph WF5201.cwl

https://github.com/Marco-Salvi/dtc51.git

Path: WF5201.cwl

Branch/Commit ID: 908abe780c8b766aea1e1e946d6063a41f494c3a
workflow graph sum-wf-noET.cwl

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

Path: tests/sum-wf-noET.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph kmer_cache_store

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5
workflow graph count-lines11-wf.cwl

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

Path: tests/count-lines11-wf.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe-dutp.cwl

Branch/Commit ID: dda9e6e06a656b7b3fa7504156474b962fe3953c
workflow graph Cell Ranger Count Gene Expression

Cell Ranger Count Gene Expression =================================

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

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

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57