Explore Workflows
View already parsed workflows here or click here to add your own
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GATKBaseRecalBQSRWorkflow_4_1_3.cwl
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https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git
Path: janis_pipelines/wgs_somatic/cwl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl Branch/Commit ID: f7f887b84734a932534ed6a4732a48852e6169d4 |
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no-outputs-wf.cwl
Workflow without outputs. |
https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/no-outputs-wf.cwl Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b |
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Build Bowtie indices
Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_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/bowtie-index.cwl Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422 |
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scatter-wf1_v1_2.cwl
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https://github.com/common-workflow-language/cwl-utils.git
Path: testdata/scatter-wf1_v1_2.cwl Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a |
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CLIP-Seq pipeline for single-read experiment NNNNG
CLIP-Seq workflow for single-read experiment. |
https://github.com/datirium/workflows.git
Path: workflows/clipseq-se.cwl Branch/Commit ID: cb5e5b8563be4977e9f2babc14fe084faa234847 |
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genome-kallisto-index.cwl
Generates a FASTA file with the DNA sequences for all transcripts in a GFF file and builds kallisto index |
https://github.com/Barski-lab/workflows.git
Path: tools/genome-kallisto-index.cwl Branch/Commit ID: a8909e86f5bcb048d136f9a7d70b4b6f8f4e485f |
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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: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081 |
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kmer_ref_compare_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_ref_compare_wnode.cwl Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d |
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scatter-wf4.cwl#main
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl Branch/Commit ID: 8010fd2bf1e7090ba6df6ca8c84bbb96e2272d32 Packed ID: main |
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record-in-secondaryFiles-missing-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/record-in-secondaryFiles-missing-wf.cwl Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf |
