Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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umi duplex alignment fastq workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/alignment_umi_duplex.cwl Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54 |
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taxonomy_check_16S
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https://github.com/ncbi/pgap.git
Path: task_types/tt_taxonomy_check_16S.cwl Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca |
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adapter for sequence_align_and_tag
Some workflow engines won't stage files in our nested structure, so parse it out here |
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e |
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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: f5c11df465aaadf712c38ba4933679fe1cbe03ca |
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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: bba6c580ab88e077f6aa2c2ee7c73159f3f9156e |
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Build STAR indices
Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome. |
https://github.com/datirium/workflows.git
Path: workflows/star-index.cwl Branch/Commit ID: 10ce6e113f749c7bd725e426445220c3bdc5ddf1 |
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Conversion and compression of RDF files
Workflow to convert a RDF file to the HDT format and GZIP compress it for long term storage |
https://git.wur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_toHDT_compression.cwl Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0 |
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running cellranger mkfastq and count
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl Branch/Commit ID: 1750cd5cc653f058f521b6195e3bec1e7df1a086 |
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RNA-Seq pipeline single-read
The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. Use 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.cwl Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca |
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tt_hmmsearch_wnode.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_hmmsearch_wnode.cwl Branch/Commit ID: 146df33e2e44afa2a608ac72c036e6b6b871af93 |
