Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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bwa_mem
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https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/bwa_mem.cwl Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48 |
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cnv_manta
CNV Manta calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/cnv_manta.cwl Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48 |
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Trim Galore RNA-Seq pipeline single-read
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.cwl Branch/Commit ID: 91bb63948c0a264334b9007ef85f936768d90d11 |
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module-1
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https://github.com/mskcc/roslin-variant.git
Path: setup/cwl/module-1.cwl Branch/Commit ID: 72353a747f45ffe35863c3b6c70b28a676a97643 |
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FASTQ Vector Removal
This workflow convert fastq to multiple fasta files |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/File-formats/fastq-to-splitted-fasta.cwl Branch/Commit ID: 8902d8d5dc85ee568decc2de51f7694164f32b00 |
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sec-wf-out.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/sec-wf-out.cwl Branch/Commit ID: 8d8512061f2367c90aac67bcbf92af1061b4af59 |
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group-isoforms-batch.cwl
Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored. |
https://github.com/Barski-lab/workflows.git
Path: tools/group-isoforms-batch.cwl Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7 |
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bam_filtering
BAM filtering |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48 |
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wffail.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/wffail.cwl Branch/Commit ID: 8d8512061f2367c90aac67bcbf92af1061b4af59 |
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SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs. |
https://github.com/Barski-lab/workflows.git
Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 12edfc2207507e53c6b5bb21e50decb5535a12f7 |
