Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
scatter-wf3_v1_0.cwl#main
|
https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/scatter-wf3_v1_0.cwl Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507 Packed ID: main |
|
|
|
WGS and MT analysis for fastq files
rna / protein - qc, preprocess, filter, annotation, index, abundance |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/wgs-noscreen-fastq.workflow.cwl Branch/Commit ID: 1844de830f6935901849ccd9966685fbf13e8042 |
|
|
|
cache_asnb_entries
|
https://github.com/ncbi/pgap.git
Path: task_types/tt_cache_asnb_entries.cwl Branch/Commit ID: 72c3091012f5c2dce38ad9213cda617d2c7a61ac |
|
|
|
step-valuefrom3-wf_v1_1.cwl
|
https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/step-valuefrom3-wf_v1_1.cwl Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355 |
|
|
|
gathered exome alignment and somatic variant detection for cle purpose
|
https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/gathered_cle_somatic_exome.cwl Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b |
|
|
|
bwa_pe.cwl
|
https://github.com/nci-gdc/gdc-dnaseq-cwl.git
Path: workflows/bamfastq_align/bwa_pe.cwl Branch/Commit ID: 6b43e8b03256492f2b36ffcf548704daaafee6f6 |
|
|
|
search.cwl#main
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/search.cwl Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684 Packed ID: main |
|
|
|
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: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081 |
|
|
|
Build STAR indices
Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome. |
https://github.com/datirium/workflows.git
Path: workflows/star-index.cwl Branch/Commit ID: 4a80f5b8f86c83af39494ecc309b789aeda77964 |
|
|
|
assemble.cwl
Assemble a set of reads using SKESA |
https://github.com/ncbi/pgap.git
Path: assemble.cwl Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d |
