Explore Workflows
View already parsed workflows here or click here to add your own
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Water bodies detection based on NDWI and the otsu threshold
Water bodies detection based on NDWI and otsu threshold applied to a single Sentinel-2 COG STAC item |
https://github.com/eoap/quickwin.git
Path: cwl-workflow/app-water-body-cloud-native.cwl Branch/Commit ID: dbc42a782afe851befdc3865488082a92ea35f29 Packed ID: main |
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rhapsody_pipeline_2.0.cwl#VDJ_Assemble_and_Annotate_Contigs_IG.cwl
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https://github.com/Chi-CRL/cwl_check_workflow.git
Path: rhapsody_pipeline_2.0.cwl Branch/Commit ID: 50ed14112f9db254034dd5530cf1a768e04eb7ff Packed ID: VDJ_Assemble_and_Annotate_Contigs_IG.cwl |
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conflict-wf.cwl#collision
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl Branch/Commit ID: 886a6ac41c685f20d39e352f9c657e59f3312265 Packed ID: collision |
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rhapsody_pipeline_2.0.cwl#VDJ_Preprocess_Reads.cwl
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https://github.com/Chi-CRL/cwl_check_workflow.git
Path: rhapsody_pipeline_2.0.cwl Branch/Commit ID: 50ed14112f9db254034dd5530cf1a768e04eb7ff Packed ID: VDJ_Preprocess_Reads.cwl |
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output-arrays-int-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/output-arrays-int-wf.cwl Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733 |
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fp_filter workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/fp_filter.cwl Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94 |
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bgzip and index VCF
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bgzip_and_index.cwl Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94 |
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Metagenomics workflow
Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflow_illumina_quality.cwl: - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - Contig binning (OPTIONAL) |
https://git.wageningenur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_metagenomics_assembly.cwl Branch/Commit ID: master |
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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: 664de58d95728edbf7d369d894f9037ebe2475fa |
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scatter-wf4.cwl#main
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/scatter-wf4.cwl Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733 Packed ID: main |
