Explore Workflows
View already parsed workflows here or click here to add your own
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RNA-Seq pipeline single-read 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 single-read** 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 single-read 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-se-dutp-mitochondrial.cwl Branch/Commit ID: 5561f7ee11dd74848680351411a19aa87b13d27b |
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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: 282762f8bbaea57dd488115745ef798e128bade1 |
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AltAnalyze ICGS
AltAnalyze ICGS =============== |
https://github.com/datirium/workflows.git
Path: workflows/altanalyze-icgs.cwl Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d |
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kmer_cache_retrieve
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_retrieve.cwl Branch/Commit ID: 4a44218a713aecc488359be275409414ae8c1434 |
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wgs alignment and tumor-only variant detection
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/tumor_only_wgs.cwl Branch/Commit ID: 25eab0390f6866ce491b44c89d9e0435d228ab6f |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: f42c889734c8f709ad2fd9090493bcaac8326c98 |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/germline_filter_vcf.cwl Branch/Commit ID: 7b4b489474473c3d2d992a838b89632c2b97dc2c |
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scatter GATK HaplotypeCaller over intervals
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl Branch/Commit ID: 7b4b489474473c3d2d992a838b89632c2b97dc2c |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf_mouse.cwl Branch/Commit ID: f42c889734c8f709ad2fd9090493bcaac8326c98 |
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bam_readcount workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_readcount.cwl Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21 |
