Explore Workflows

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

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

Path: subworkflows/allele-vcf-alignreads-se-pe.cwl

Branch/Commit ID: 2d00e7f29c72d33b70dcd46b58db1fc31a7f2d86

https://github.com/mscheremetjew/workflow-is-cwl.git

Path: workflows/TranscriptsAnnotation-i5only-wf.cwl

Branch/Commit ID: b32b610cde3524e628d1c7370a21d167da19470c

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

Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b

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

Path: definitions/pipelines/umi_duplex_alignment.cwl

Branch/Commit ID: 641083e9ed933d388f36fa04c00c20a810599e94

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

Path: spurious_annot/wf_spurious_annot_pass2.cwl

Branch/Commit ID: c009eeba7379efbbd37b8d5013a83f161f06939b

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: 0d2f354af9192a56af258a7d2426c7c160f4ec1a

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: 69c0f25d08cfa02d8bfaa85ce5d70dd14cc52e3f

Devel version of Single-Cell Advanced Cell Ranger Pipeline (SoupX) =================================================================

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

Path: workflows/soupx.cwl

Branch/Commit ID: 92f1a6da9c4f85fb51340b01b32373a50fde0891

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/module-2.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf

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: 664de58d95728edbf7d369d894f9037ebe2475fa