Explore Workflows

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Graph Name Retrieved From View
workflow graph allele-alignreads-se-pe.cwl

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/Barski-lab/workflows.git

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

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
workflow graph indices-header.cwl

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

Path: metadata/indices-header.cwl

Branch/Commit ID: 99840925c38f8a3d9cdf9d2c7f2f032e083bfd01
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/exome.cwl

Branch/Commit ID: d2c2f2eb846ae2e9cdcab46e3bb88e42126cb3f5
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f
workflow graph Run tRNAScan

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

Path: bacterial_trna/wf_trnascan.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f
workflow graph Run genomic CMsearch (Rfam rRNA)

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f
workflow graph Create Genomic Collection for Bacterial Pipeline, ASN.1 input

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

Path: genomic_source/wf_genomic_source_asn.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f
workflow graph spurious_annot pass2

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

Path: spurious_annot/wf_spurious_annot_pass2.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f
workflow graph spurious_annot

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

Path: spurious_annot/wf_spurious_annot_pass1.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f
workflow graph Non-Coding Bacterial Genes

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

Path: bacterial_noncoding/wf_bacterial_noncoding.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f