Explore Workflows
View already parsed workflows here or click here to add your own
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assm_assm_blastn_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f |
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Run genomic CMsearch (Rfam rRNA)
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https://github.com/ncbi/pgap.git
Path: bacterial_ncrna/wf_gcmsearch.cwl Branch/Commit ID: 5ec226c941562124032ca6861bc8d1aeabf9d91a |
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bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow. |
https://github.com/datirium/workflows.git
Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: 77970404d7c704cba965ae646582e19e5d76aabe |
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Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass2.cwl Branch/Commit ID: 5ec226c941562124032ca6861bc8d1aeabf9d91a |
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Run tRNAScan
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https://github.com/ncbi/pgap.git
Path: bacterial_trna/wf_trnascan.cwl Branch/Commit ID: 5ec226c941562124032ca6861bc8d1aeabf9d91a |
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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: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f |
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WGS and MT analysis for fastq files
rna / protein - qc, preprocess, filter, annotation, index, abundance |
https://github.com/MG-RAST/pipeline.git
Path: CWL/Workflows/wgs-fasta.workflow.cwl Branch/Commit ID: 7b1df2ecce5a8727f2c546c5baa45c919edd8a76 |
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Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass3.cwl Branch/Commit ID: 5ec226c941562124032ca6861bc8d1aeabf9d91a |
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umi molecular alignment fastq workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/alignment_umi_molecular.cwl Branch/Commit ID: bed420556091b7b8b45cf20a95e5947e1de9a416 |
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kmer_seq_entry_extract_wnode
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl Branch/Commit ID: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f |
