Explore Workflows

https://github.com/ncbi/pgap.git

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 4def84df33963fc9ac9d5c5f804b911d01a0d9ad

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944

Packed ID: main

https://github.com/datirium/workflows.git

Path: subworkflows/chipseq-gen-bigwig.cwl

Branch/Commit ID: cb5e5b8563be4977e9f2babc14fe084faa234847

Note: should be updated 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-dutp.cwl

Branch/Commit ID: 4ab9399a4777610a579ea2c259b9356f27641dcc

https://github.com/datirium/workflows.git

Path: subworkflows/allele-process-reference.cwl

Branch/Commit ID: 2d00e7f29c72d33b70dcd46b58db1fc31a7f2d86

https://github.com/datirium/workflows.git

Path: metadata/rnaseq-header.cwl

Branch/Commit ID: a179b226d17177dd32a3f9d1a24a895f33c42b38

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: gdc-dnaseq-aln-cwl/gdc_dnaseq.bamfastq_align.workflow.cwl

Branch/Commit ID: 234f6745856802a47fb3c27ee273253caa39f39e

https://github.com/biosciencedbc/jga-analysis.git

Path: per-sample/Workflows/gridss-germline.cwl

Branch/Commit ID: 651b97b982a48cdb4e5f36edc0b1f38b25b30c10

Devel version of Single-Cell Preprocessing Pipeline ===================================================

https://github.com/datirium/workflows.git

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_create_readme/readme-genePrediction-workflow.cwl

Branch/Commit ID: add45db6f08de518e224bdc3c04094fd69cad2d2