Explore Workflows
View already parsed workflows here or click here to add your own
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Illumina read quality control, trimming and contamination filter.
**Workflow for Illumina paired read quality control, trimming and filtering.**<br /> Multiple paired datasets will be merged into single paired dataset.<br /> Summary: - FastQC on raw data files<br /> - fastp for read quality trimming<br /> - BBduk for phiX and (optional) rRNA filtering<br /> - Kraken2 for taxonomic classification of reads (optional)<br /> - BBmap for (contamination) filtering using given references (optional)<br /> - FastQC on filtered (merged) data<br /> **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default |
![]() Path: cwl/workflows/workflow_illumina_quality.cwl Branch/Commit ID: master |
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step-valuefrom2-wf.cwl
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![]() Path: tests/step-valuefrom2-wf.cwl Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733 |
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bqsr-distr.cwl
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![]() Path: stage/bqsr-distr.cwl Branch/Commit ID: d20382adfe7285cb517a25d95d2bcb7586546e23 |
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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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calculate_contamination_workflow.cwl
GATK4.1.2 Calculate tumor-normal contamination workflow |
![]() Path: subworkflows/calculate_contamination_workflow.cwl Branch/Commit ID: 138d484362084dfc97d9fb7d839855b4bc2c5599 |
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Indices builder from GBOL RDF (TTL)
Workflow to build different indices for different tools from a genome and transcriptome. This workflow expects an (annotated) genome in GBOL ttl format. Steps: - SAPP: rdf2gtf (genome fasta) - SAPP: rdf2fasta (transcripts fasta) - STAR index (Optional for Eukaryotic origin) - bowtie2 index - kallisto index |
![]() Path: cwl/workflows/workflow_indexbuilder.cwl Branch/Commit ID: master |
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workflowSegment.cwl
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![]() Path: saber/i2g/examples/I2G_Seg_Workflow/workflowSegment.cwl Branch/Commit ID: 051b9506fd7356113be013ac3c435a101fd95123 |
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extract_gencoll_ids
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![]() Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f |
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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 |
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ACCESS_pipeline.cwl
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![]() Path: workflows/ACCESS_pipeline.cwl Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf |