Explore Workflows
View already parsed workflows here or click here to add your own
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Genome conversion and annotation
Workflow for genome annotation from EMBL format |
Path: cwl/workflows/workflow_sapp_microbes.cwl Branch/Commit ID: master |
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Quality assessment, amplicon classification
Workflow for quality assessment of paired reads and classification using NGTax 2.0. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Export module |
Path: cwl/workflows/workflow_ngtax.cwl Branch/Commit ID: master |
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Metagenomics workflow
Workflow pilon assembly polishing Steps: - BBmap (Read mapping to assembly) - Pilon |
Path: cwl/workflows/workflow_pilon_mapping.cwl Branch/Commit ID: master |
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Quality assessment, amplicon classification and functional prediction
Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Picrust 2 - Export module for ngtax |
Path: cwl/workflows/workflow_ngtax_picrust2.cwl Branch/Commit ID: master |
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kmer_seq_entry_extract_wnode
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Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl Branch/Commit ID: 4cd1fb565519fbe5f9c462acae01ff608c3784a3 |
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SAMSA2 pipeline
SAMSA2 complete workflow for meta-omics read annotation Steps: - Diamond read blastx - Refseq - SEED - SAMSA2 processing |
Path: cwl/workflows/workflow_samsa2.cwl Branch/Commit ID: master |
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basename-fields-test.cwl
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Path: tests/basename-fields-test.cwl Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4 |
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merge and annotate svs with population allele freq and vep
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Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: c235dc6d623879a6c4f5fb307f545c9806eb2d23 |
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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) |
Path: cwl/workflows/workflow_metagenomics_assembly.cwl Branch/Commit ID: master |
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Spliced RNAseq workflow
Workflow for Spliced RNAseq data Steps: - workflow_illumina_quality: - FastQC (Read Quality Control) - fastp (Read Trimming) - STAR (Read mapping) - featurecounts (transcript read counts) - kallisto (transcript [pseudo]counts) |
Path: cwl/workflows/workflow_RNAseq_Spliced.cwl Branch/Commit ID: master |
