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Graph Name Retrieved From View
workflow graph Bismark Methylation - pipeline for BS-Seq data analysis

Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).

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

Path: workflows/bismark-methylation-se.cwl

Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca
workflow graph host.sort.workflow.cwl

https://github.com/azzaea/cwl-scalability-vis.git

Path: host.sort.workflow.cwl

Branch/Commit ID: d79d09f92c64e25d1a68af7e8aed5e48e73e6537
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: bba6c580ab88e077f6aa2c2ee7c73159f3f9156e
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: ffd73951157c61c1581d346628d75b61cdd04141
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: ffd73951157c61c1581d346628d75b61cdd04141
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: 7f857f7f2d7c080d27c775b67a6d6f7d94bce31f
workflow graph RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
workflow graph 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: 441b85003fdc10cf4cbf333d89acb4d23b0fef32
workflow graph Raw sequence data to BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: f5c11df465aaadf712c38ba4933679fe1cbe03ca