Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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count-lines1-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/count-lines1-wf.cwl Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb |
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kmer_cache_store
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: c18a7e5164cb6b19f06b3d1e869407c118a87f7e |
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ani_top_n
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https://github.com/ncbi/pgap.git
Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: c18a7e5164cb6b19f06b3d1e869407c118a87f7e |
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count-lines1-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb |
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kmer_build_tree
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_build_tree.cwl Branch/Commit ID: 664e99a23a3ed4ba36c08323ac597c4fbcd88df1 |
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blastp_wnode_naming
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https://github.com/ncbi/pgap.git
Path: task_types/tt_blastp_wnode_naming.cwl Branch/Commit ID: c18a7e5164cb6b19f06b3d1e869407c118a87f7e |
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Generate genome indices for STAR & bowtie
Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files |
https://github.com/datirium/workflows.git
Path: workflows/genome-indices.cwl Branch/Commit ID: 8049a781ac4aae579fbd3036fa0bf654532f15be |
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Pairwise genomic regions intersection
Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments |
https://github.com/datirium/workflows.git
Path: workflows/peak-intersect.cwl Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620 |
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SAMSA2 pipeline
SAMSA2 complete workflow for meta-omics read annotation Steps: - Diamond read blastx - Refseq - SEED - SAMSA2 processing |
https://git.wur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_samsa2.cwl Branch/Commit ID: cd0c19d51068c5407cd70b718a561d4662819d87 |
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Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific
https://chipster.csc.fi/manual/library-type-summary.html Modified 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-smarter-dutp.cwl Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620 |
