Explore Workflows

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 664de58d95728edbf7d369d894f9037ebe2475fa

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: 64f7fe4438898218fd83133efa25251078f5b27e

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: 861d9baa067af98d794ba0ed4e43aa42e37d8a24

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: 64f7fe4438898218fd83133efa25251078f5b27e

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 0e8110083bad6ea98fc487aa262953a6c5e010b5

Packed ID: main

A basic differential methylation analysis workflow using BismarkCov formatted bed files as input to the RnBeads tool. Analysis is conducted on region and sites levels according to the sample groups specified by user (limited to 2 conditions in this workflow implementation). See report html files for detailed descriptions of analyses and results interpretation. ### __Inputs__ *General Info:* - Experiment short name/Alias* - a unique name for the sample (e.g. what was used on tubes while processing it) - Condition 1 name - name defining condition/group 1 - Condition 2 name - name defining condition/group 2 - Bismark coverage files* for condition1 - minumum of 2 is required for analysis - Bismark coverage files* for condition2 - minumum of 2 is required for analysis - Sample genome - available options: hg19, hg38, mm9, mm10, rn5 - Genome type - indicate mismark index used for upstream samples (input for conditions 1 and 2) *Advanced:* - Number of threads for steps that support multithreading - default set to `4` *[BismarkCov formatted bed](https://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_User_Guide.pdf): The genome-wide cytosine report (optional) is tab-delimited in the following format (1-based coords): <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context> ### __Outputs__ Intermediate and final downloadable outputs include: - sig_dm_sites.bed ([bed for IGV](https://genome.ucsc.edu/FAQ/FAQformat.html#format1); sig diff meth sites) - sig_dm_sites_annotated.tsv (tsv for TABLE; for each site above, closest single gene annotation) - Site_id, unique indentifer per methylated site - Site_Chr, chromosome of methylated site - Site_position, 1-based position in chr of methylated site - Site_strand, strand of methylated site - Log2_Meth_Quotient, log2 of the quotient in methylation: log2((mean.g1+epsilon)/(mean.g2+epsilon)), where epsilon:=0.01. In case of paired analysis, it is the mean of the pairwise quotients. - FDR, adjusted p-values, all <0.10 assumed to be significant - Coverage_score, value between 0-1000 reflects strength of mean coverage difference between conditions and equals [1000-(1000/(meancov_g1-meancov_g2)^2](https://www.wolframalpha.com/input?i=solve+1000-%281000%2F%28x%5E2%29%29), if meancov_g1-meancov_g2==0, score=0, elif score<1==1, else score - meancov_g1, mean coverage of condition1 - meancov_g2, mean coverage of condition2 - refSeq_id, RefSeq gene id - Gene_id, gene symbol - Chr, gene chromosome - txStart, gene transcription start position - tsEnd, gene transcription end position - txStrand, gene strand - stdout and stderr log files - Packaged RnBeads reports directory (reports.tar.gz) contains: reports/ ├── configuration ├── data_import.html ├── data_import_data ├── data_import_images ├── data_import_pdfs ├── differential_methylation.html ├── differential_methylation_data ├── differential_methylation_images ├── differential_methylation_pdfs ├── preprocessing.html ├── preprocessing_data ├── preprocessing_images ├── preprocessing_pdfs ├── quality_control.html ├── quality_control_data ├── quality_control_images ├── quality_control_pdfs ├── tracks_and_tables.html ├── tracks_and_tables_data ├── tracks_and_tables_images └── tracks_and_tables_pdfs Reported methylation is in the form of regions (genes, promoters, cpg, tiling) and specific sites: - genes - Ensembl gene definitions are downloaded using the biomaRt package. - promoters - A promoter is defined as the region spanning 1,500 bases upstream and 500 bases downstream of the transcription start site of the corresponding gene - cpg - the CpG islands from the UCSC Genome Browser - tiling - a window size of 5 kilobases are defined over the whole genome - sites - all cytosines in the context of CpGs in the respective genome ### __Data Analysis Steps__ 1. generate sample sheet with associated conditions for testing in RnBeads 2. setup rnbeads analyses in R, and run differential methylation analysis 3. process output diffmeth files for regions and sites 4. find single closest gene annotations for all significantly diffmeth sites 5. package and save rnbeads report directory 6. clean up report dir for html outputs ### __References__ - https://rnbeads.org/materials/example_3/differential_methylation.html - Makambi, K. (2003) Weighted inverse chi-square method for correlated significance tests. Journal of Applied Statistics, 30(2), 225234 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216143/ - Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C. Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods. 2014 Nov;11(11):1138-1140. doi: 10.1038/nmeth.3115. Epub 2014 Sep 28. PMID: 25262207; PMCID: PMC4216143.

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

Path: workflows/diffmeth.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

Cell Ranger Multi Gene Expression and V(D)J Repertoire Profiling Quantifies gene expression and performs profiling of V(D)J repertoire from a single GEM well

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

Path: workflows/cellranger-multi.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca

### 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: c6bfa0de917efb536dd385624fc7702e6748e61d

Filter DiffBind results for deepTools heatmap analysis ====================================================== Filter differentially bound sites from DiffBind analysis to be used with deepTools heatmap analysis

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

Path: workflows/filter-diffbind-for-heatmap.cwl

Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e