Explore Workflows

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

Graph Name Retrieved From View
workflow graph bwa_mem

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

Path: structuralvariants/cwl/subworkflows/bwa_mem.cwl

Branch/Commit ID: 6ccec9c5c5bc9fb4e75ca0b9cc22d13df9ffb815
workflow graph Trim Galore 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 **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.cwl

Branch/Commit ID: 42dc4f70b117e78785b82865ec4c4b941ac1c259
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/exome.cwl

Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5
workflow graph indexing_bed

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

Path: structuralvariants/subworkflows/indexing_bed.cwl

Branch/Commit ID: c84d205c8239b7dea9d1b49e3e166973c3ebcd66
workflow graph gather AML trio outputs

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

Path: definitions/pipelines/aml_trio_cle_gathered.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379
workflow graph count-lines10-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: 65aedc5e7e1f3ccace7f9022f8a54b3f0d5c9a8c
workflow graph count-lines8-wf-noET.cwl

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

Path: tests/count-lines8-wf-noET.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: ea8c2aea64cab2241e02f4cb60ca9ca7593dfa58
workflow graph steplevel-resreq.cwl

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

Path: tests/steplevel-resreq.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3