Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
Trim Galore RNA-Seq pipeline paired-end strand specific
Modified 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-dutp.cwl Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5 |
|
|
|
816_wf.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/816_wf.cwl Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb |
|
|
|
QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data
### Devel version of QuantSeq 3' FWD, FWD-UMI or REV for single-read mRNA-Seq data |
https://github.com/datirium/workflows.git
Path: workflows/trim-quantseq-mrnaseq-se-strand-specific.cwl Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620 |
|
|
|
bam-bedgraph-bigwig.cwl
Workflow converts input BAM file into bigWig and bedGraph files |
https://github.com/datirium/workflows.git
Path: subworkflows/bam-bedgraph-bigwig.cwl Branch/Commit ID: c602e3cdd72ff904dd54d46ba2b5146eb1c57022 |
|
|
|
wffail.cwl
|
https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/wffail.cwl Branch/Commit ID: 0e8110083bad6ea98fc487aa262953a6c5e010b5 |
|
|
|
allele-process-strain.cwl
|
https://github.com/datirium/workflows.git
Path: subworkflows/allele-process-strain.cwl Branch/Commit ID: 00ced0fc44ceeb3495e891232e1000235e56ee6b |
|
|
|
kmer_cache_store
|
https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: b0ee40d34d233f1611c2e2c66b6d22a3b7deec05 |
|
|
|
scatter-valuefrom-wf4.cwl#main
|
https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl Branch/Commit ID: fc6ca8b1498926f705dcfde7ab0a365bd09a9675 Packed ID: main |
|
|
|
Single-cell Reference Indices
Single-cell Reference Indices Builds a Cell Ranger and Cell Ranger ARC compatible reference folders from the custom genome FASTA and gene GTF annotation files |
https://github.com/Barski-lab/sc-seq-analysis.git
Path: workflows/sc-ref-indices-wf.cwl Branch/Commit ID: e70b7fab45e4bd2abfb7dab2b8b1f79ce904ac69 |
|
|
|
RNA-seq (VCF) alelle specific pipeline for paired-end data
Allele specific RNA-Seq (using vcf) paired-end workflow |
https://github.com/datirium/workflows.git
Path: workflows/allele-vcf-rnaseq-pe.cwl Branch/Commit ID: c602e3cdd72ff904dd54d46ba2b5146eb1c57022 |
