Explore Workflows

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Graph Name Retrieved From View
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph qa_check_subwf.cwl

This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs

https://github.com/icgc-tcga-pancancer/oxog-dockstore-tools.git

Path: qa_check_subwf.cwl

Branch/Commit ID: 6366ed398da10019b6d81a789291af6d909f28f4
workflow graph assemble.cwl

Assemble a set of reads using SKESA

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

Path: assemble.cwl

Branch/Commit ID: af78bfbc7625a817a2875e87c8ee267cf46b8c57
workflow graph steplevel-resreq.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/steplevel-resreq.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de
workflow graph merge and annotate svs with population allele freq and vep

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph workflow.cwl

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

Path: flow_dispatch/workflow.cwl

Branch/Commit ID: 5910b4d88aca172252d9102ddb610a7dc9e1347f
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
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: e99e80a2c19682d59947bde04a892d7b6d90091c
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 2c7879b47890b9300ab9b5ebd35e17372e077757