Explore Workflows
View already parsed workflows here or click here to add your own
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mut2.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/mut2.cwl Branch/Commit ID: 12993a6eb60f5ccb4edbe77cb6de661cfc496090 |
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allele-vcf-alignreads-se-pe.cwl
Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted. |
https://github.com/datirium/workflows.git
Path: subworkflows/allele-vcf-alignreads-se-pe.cwl Branch/Commit ID: 00ced0fc44ceeb3495e891232e1000235e56ee6b |
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trim-rnaseq-se.cwl
Runs RNA-Seq BioWardrobe basic analysis with single-end data file. |
https://github.com/datirium/workflows.git
Path: workflows/trim-rnaseq-se.cwl Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf |
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scatterfail.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/scatterfail.cwl Branch/Commit ID: 4635090ef98247b1902b3c7a25c007d9db1cb883 |
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rnaseq-se-dutp-mitochondrial.cwl
RNA-Seq strand specific mitochondrial workflow for single-read experiment based on BioWardrobe's basic analysis. |
https://github.com/datirium/workflows.git
Path: workflows/rnaseq-se-dutp-mitochondrial.cwl Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf |
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rnaseq-pe.cwl
RNA-Seq basic analysis workflow for paired-end experiment. |
https://github.com/datirium/workflows.git
Path: workflows/rnaseq-pe.cwl Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf |
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env-wf1.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl Branch/Commit ID: 7bfd77118cdc80dd7150115dd7a1a7ee6046f6fe |
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Trim Galore RNA-Seq pipeline single-read strand specific
Note: should be updated 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-dutp.cwl Branch/Commit ID: 92f1a6da9c4f85fb51340b01b32373a50fde0891 |
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Cell Ranger Build Reference Indices
Devel version of Cell Ranger Build Reference Indices pipeline ============================================================= |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-mkref.cwl Branch/Commit ID: 8a92669a566589d80fde9d151054ffc220ed4ddd |
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ChIP-Seq pipeline single-read
ChIP-Seq basic analysis workflow for a single-read experiment. |
https://github.com/datirium/workflows.git
Path: workflows/chipseq-se.cwl Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf |
