Explore Workflows
View already parsed workflows here or click here to add your own
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tt_blastn_wnode
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Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: 16e3915d2a357e2a861b30911c832e5ddc0c1784 |
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trimmed_fastq
Quality Control and Raw Data trimming |
Path: structuralvariants/subworkflows/trimmed_fastq.cwl Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3 |
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mut2.cwl
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Path: tests/wf/mut2.cwl Branch/Commit ID: 83038feb2a6fc3bab952e1ecc2a11bfbc8c557b4 |
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indices-header.cwl
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Path: metadata/indices-header.cwl Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2 |
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timelimit3-wf.cwl
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Path: tests/timelimit3-wf.cwl Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df |
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step-valuefrom3-wf_v1_2.cwl
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Path: testdata/step-valuefrom3-wf_v1_2.cwl Branch/Commit ID: 77669d4dd1d1ebd2bdd9810f911608146d9b8e51 |
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heatmap-prepare.cwl
Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order. |
Path: subworkflows/heatmap-prepare.cwl Branch/Commit ID: 4106b7dc96e968db291b7a61ecd1641aa3b3dd6d |
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BWA index pipeline
This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760. |
Path: workflows/bwa-index.cwl Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67 |
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directory.cwl
Inspect provided directory and return filenames. Generate a new directory and return it (including content). |
Path: tests/wf/directory.cwl Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534 |
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Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)
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Path: bacterial_annot/wf_bacterial_annot_pass1.cwl Branch/Commit ID: 343cb00abda2bc06daf9a32e1386c835f324ae6e |
