Explore Workflows

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

Graph Name Retrieved From View
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: 6a29751f2b16659c1592f1e94837c989e68f3b8b
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe
workflow graph schemadef-wf.cwl

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

Path: tests/schemadef-wf.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph samtools_sort

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/samtools_sort.cwl

Branch/Commit ID: c84d205c8239b7dea9d1b49e3e166973c3ebcd66
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_duplex.cwl

Branch/Commit ID: 449bc7e45bb02316d040f73838ef18359e770268
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 1560e7817fdb71d58aca7f98aba68809d840ade1
workflow graph cnv_manta

CNV Manta calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/cnv_manta.cwl

Branch/Commit ID: c84d205c8239b7dea9d1b49e3e166973c3ebcd66
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: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: 449bc7e45bb02316d040f73838ef18359e770268
workflow graph kfdrc_alignment_pipeline.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: dev/pilot-run/worklflows/kfdrc_alignment_pipeline.cwl

Branch/Commit ID: 64fee04b683c95720227d340a714b2ee73f21c5f