Explore Workflows

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

Graph Name Retrieved From View
workflow graph Unaligned bam to sorted, markduped bam

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 7f9dfad8e45ca096ae738cff646195b2b1ba7d7f
workflow graph Sounder SIPS L1B PGE

Processes Sounder SIPS L1A products into L1B Products

 https://github.com/unity-sds/unity-sps-workflows.git

Path: sounder_sips/l1b_package.cwl

Branch/Commit ID: 90ef1fab4fbfb6622407eaf6fe902aec5024c376

Packed ID: main
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph timelimit2-wf.cwl

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

Path: tests/timelimit2-wf.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph step_valuefrom5_wf_with_id_v1_2.cwl

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

Path: testdata/step_valuefrom5_wf_with_id_v1_2.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 293dc7b83639d21a56efff2baf9dfe4e97b9b806
workflow graph stdout-wf_v1_0.cwl

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

Path: testdata/stdout-wf_v1_0.cwl

Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed 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. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-mitochondrial.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895