Explore Workflows
View already parsed workflows here or click here to add your own
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Trim Galore 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-end** 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-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. 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/trim-rnaseq-se.cwl Branch/Commit ID: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726 |
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js_output_workflow.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/js_output_workflow.cwl Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375 |
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hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather
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https://github.com/ncbi/pgap.git
Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl Branch/Commit ID: 1ce371c7412debef75edf09e8830d74ac987a668 |
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mut3.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/mut3.cwl Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684 |
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align_sort_sa
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https://github.com/ncbi/pgap.git
Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: 6d8d29a2156b93a75f1d1c6952738bd63f6bd98e |
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igv-report_maf_workflow.cwl
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/igv-report_maf_workflow.cwl Branch/Commit ID: 462f6015c9268a4205b6e81de018a470b8a4a153 |
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Cell Ranger Build V(D)J Reference Indices
Cell Ranger Build V(D)J Reference Indices Build a Cell Ranger V(D)J-compatible reference folder from a user-supplied genome FASTA and gene GTF files. |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-mkvdjref.cwl Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf |
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downsample unaligned BAM and align
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5 |
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step-valuefrom-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40 |
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Trim Galore RNA-Seq pipeline paired-end
The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** 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-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. 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 files 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/trim-rnaseq-pe.cwl Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f |
