Explore Workflows

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

Graph Name Retrieved From View
workflow graph Alignment without BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl

Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 3a287b7cb6162cdea79865235d224fea45963d87
workflow graph picard_markduplicates

Mark duplicates

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

Path: structuralvariants/cwl/abstract_operations/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 3f6a871f81f343cf81a345f73ff2eeac70804b8c
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
workflow graph Transcriptome assembly workflow

https://github.com/mscheremetjew/workflow-is-cwl.git

Path: workflows/TranscriptomeAssembly-wf.cwl

Branch/Commit ID: 264176e422f93fe61ba3a08874a50266e7b48df8
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: 5e7385b8cfa4ddae822fff37b6bd22eb0370b389
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa
workflow graph Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: 8a92669a566589d80fde9d151054ffc220ed4ddd
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: add6b7724698694e0e72d972e2e85e1ae4e67902
workflow graph 5S-from-tablehits.cwl

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/5S-from-tablehits.cwl

Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193