Explore Workflows

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

Graph Name Retrieved From View
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 1bf7dc7b03ea3c64e54375cc5c3767849a801000
workflow graph abundance

abundace profiles from annotated files, for protein and/or rna

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/abundance.workflow.cwl

Branch/Commit ID: f5839797da8209a9d3e441023f88130219751020
workflow graph rna annotation

RNAs - predict, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/rna-annotation.workflow.cwl

Branch/Commit ID: f5839797da8209a9d3e441023f88130219751020
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 146df33e2e44afa2a608ac72c036e6b6b871af93
workflow graph Long-covid.cwl

https://github.com/cwlviewer-test/Long-covid---aedea650-7a21-11ed-b9d2-e51f21933d80-1.git

Path: Long-covid---9c236c30-7a21-11ed-b9d2-e51f21933d80/Long-covid.cwl

Branch/Commit ID: read-potential-cases-disc
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: ffd73951157c61c1581d346628d75b61cdd04141
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0
workflow graph running cellranger mkfastq and count

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

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: 441b85003fdc10cf4cbf333d89acb4d23b0fef32
workflow graph alignment_novoalign_multi_readgroup.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/alignment_novoalign_multi_readgroup.cwl

Branch/Commit ID: 3c62f1ddf8a54601da3cfc16c37d0cb0d6a2ea28
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: d1bef74924efcb8bfaa00987b3f148d5a192b7a9