Explore Workflows

CNV Manta calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/cnv_manta.cwl

Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3

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

Path: bacterial_trna/wf_scan_and_dump.cwl

Branch/Commit ID: cb15f907132fb90bc66b39bb0af3c211801feba1

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 60edaf6f57eaaf02cda1a3d8cb9a825aa64a43e2

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 4700fbee9a5a3271eef8bc9ee595619d0720431b

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: e81df43c40bc6849ece095a05cb0247dc53b94b1

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_alignment_wf.cwl

Branch/Commit ID: e75f0c96153a484db1f882f6ff2a9764519a3179

https://chipster.csc.fi/manual/library-type-summary.html 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-smarter-dutp.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2

1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump) 2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files) 3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ files to reference genome, calculate genes and isoforms expression (run RSEM) 5. Count mapped reads number in sorted BAM file (run bamtools stats) 6. Generate genome coverage BED file (run bedtools genomecov) 7. Sort genearted BED file (run sort) 8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-rnaseq-se.cwl

Branch/Commit ID: dda9e6e06a656b7b3fa7504156474b962fe3953c

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: cb15f907132fb90bc66b39bb0af3c211801feba1

Simulation steps pipeline

https://github.com/ILIAD-ocean-twin/application_package.git

Path: workflow_in_workflow/workflow_same_level_v2.cwl

Branch/Commit ID: 9a0db98839bbc655e12d49f56c61deecd77ff14c

Packed ID: main_pipeline