Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
bam to trimmed fastqs and biscuit alignments
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6 |
|
|
|
Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d |
|
|
|
format_rrnas_from_seq_entry
|
https://github.com/ncbi/pgap.git
Path: task_types/tt_format_rrnas_from_seq_entry.cwl Branch/Commit ID: cabb1a9a95244e93294727be8cf5816c38992cb0 |
|
|
|
exome alignment and tumor-only variant detection
|
https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/tumor_only_exome.cwl Branch/Commit ID: 8dc462a7d9ba1479f764682af99c69d8574cb3dc |
|
|
|
SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs. |
https://github.com/datirium/workflows.git
Path: tools/soupx-subworkflow.cwl Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e |
|
|
|
Unaligned BAM to BQSR and VCF
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl Branch/Commit ID: a3e26136043c03192c38c335316d2d36e3e67478 |
|
|
|
exome alignment and germline variant detection
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6 |
|
|
|
Bisulfite QC tools
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bisulfite_qc.cwl Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6 |
|
|
|
RNA-Seq pipeline single-read stranded mitochondrial
Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-dutp-mitochondrial.cwl Branch/Commit ID: 3fc68366adb179927af5528c27b153abaf94494d |
|
|
|
count-lines5-wf.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl Branch/Commit ID: 875b928ce50a3202f5954843b79ea86683c160fa |
