Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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cnv_exomedepth
CNV ExomeDepth calling |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3 |
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final_filtering
Final filtering |
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/abstract_operations/subworkflows/final_filtering.cwl Branch/Commit ID: f4c51a054b1ec51d07d89c6a8218e610653675f3 |
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HS Metrics workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/hs_metrics.cwl Branch/Commit ID: 258bd4353ad1ca7790b3ae626bf42ab8194e7561 |
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Exome QC workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5 |
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running cellranger mkfastq and count
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl Branch/Commit ID: 6bfb64375e7ebb6eb40f463ede86d8deccdb9eff |
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RNA-Seq pipeline paired-end stranded mitochondrial
Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-pe-dutp-mitochondrial.cwl Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058 |
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Filter differentially expressed genes from DESeq for Tag Density Profile Analyses
Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses. |
https://github.com/datirium/workflows.git
Path: workflows/filter-deseq-for-heatmap.cwl Branch/Commit ID: 2caa50434966ebdf4b33e5ca689c2e4df32f9058 |
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cache_asnb_entries
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https://github.com/ncbi/pgap.git
Path: task_types/tt_cache_asnb_entries.cwl Branch/Commit ID: 6d04f5d65d1d4893706d9ae7e27341633333054f |
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MEME motif
This workflow uses MEME suite for motif finding |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/ChIP-Seq/meme-motif.cwl Branch/Commit ID: e1c19e64f6fc210f65472ee227786d33c9b4909a |
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tt_blastn_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: 909f26beaf96c2cdfe208f87ecd1e9c3de20b81c |
