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pipelines
Travis CI User edited this page Sep 1, 2020
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| CWL | Description |
|---|---|
| alignment_exome.cwl | exome alignment with qc |
| alignment_exome_nonhuman.cwl | exome alignment with qc, no bqsr, no verify_bam_id |
| alignment_umi_duplex.cwl | umi duplex alignment fastq workflow |
| alignment_umi_molecular.cwl | umi molecular alignment fastq workflow |
| alignment_wgs.cwl | wgs alignment with qc |
| alignment_wgs_nonhuman.cwl | alignment for nonhuman with qc |
| aml_trio_cle.cwl | Replace legacy AML Trio Assay |
| aml_trio_cle_gathered.cwl | gather AML trio outputs |
| bisulfite.cwl | Bisulfite alignment and QC |
| chipseq.cwl | Chipseq alignment with qc and creating homer tag directory |
| chipseq_alignment_nonhuman.cwl | Chipseq alignment for nonhuman with qc and creating homer tag directory |
| detect_variants.cwl | Detect Variants workflow |
| detect_variants_nonhuman.cwl | Detect Variants workflow |
| detect_variants_wgs.cwl | Detect Variants workflow for WGS pipeline |
| downsample_and_recall.cwl | Downsample and HaplotypeCaller |
| gathered_downsample_and_recall.cwl | Gathered Downsample and HaplotypeCaller |
| germline_exome.cwl | exome alignment and germline variant detection |
| germline_exome_gvcf.cwl | exome alignment and germline variant detection |
| germline_exome_hla_typing.cwl | exome alignment and germline variant detection, with optitype for HLA typing |
| germline_wgs.cwl | wgs alignment and germline variant detection |
| germline_wgs_gvcf.cwl | wgs alignment and germline variant detection |
| immuno.cwl | Immunotherapy Workflow |
| panel_of_normals.cwl | mutect panel-of-normals workflow |
| rnaseq.cwl | RNA-Seq alignment and transcript/gene abundance workflow |
| rnaseq_star_fusion.cwl | STAR-RNA-Seq alignment and transcript/gene abundance workflow |
| rnaseq_star_fusion_with_xenosplit.cwl | STAR-RNA-Seq alignment and transcript/gene abundance workflow with Xenosplit |
| somatic_exome.cwl | somatic_exome: exome alignment and somatic variant detection |
| somatic_exome_cle.cwl | exome alignment and somatic variant detection for cle purpose |
| somatic_exome_cle_gathered.cwl | gathered exome alignment and somatic variant detection for cle purpose |
| somatic_exome_gathered.cwl | gathered exome alignment and somatic variant detection |
| somatic_exome_nonhuman.cwl | exome alignment and somatic variant detection |
| somatic_wgs.cwl | Whole genome alignment and somatic variant detection |
| tumor_only_detect_variants.cwl | Tumor-Only Detect Variants workflow |
| tumor_only_exome.cwl | exome alignment and tumor-only variant detection |
| tumor_only_wgs.cwl | wgs alignment and tumor-only variant detection |