pipelines_rnaseq_star_fusion_with_xenosplit.cwl
APipe Tester edited this page Apr 6, 2022
·
12 revisions
This page is auto-generated. Do not edit.
STAR-RNA-Seq alignment and transcript/gene abundance workflow with Xenosplit
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| reference | ['string', 'File'] | ['.fai', '^.dict'] | ||
| unaligned | ../types/sequence_data.yml#sequence_data[] | |||
| outsam_attrrg_line | string[] | |||
| graft_star_genome_dir | Location of the STAR reference for the graft species (usually human) | Directory | ||
| graft_outfile_name_prefix | Prefix name for the graft bam (often 'human') | string? | ||
| host_star_genome_dir | Location of the STAR reference for the host species (usually mouse) | Directory | ||
| host_outfile_name_prefix | Prefix name for the host bam (often 'mouse') | string? | ||
| star_fusion_genome_dir | star fusion directory for the graft species (often human) - fusions are only called on the xenograft-filtered bam | Directory | ||
| graft_gtf_file | GTF file corresponding the to the graft species (often human) | File | ||
| host_gtf_file | GTF file corresponding the to the host species (often mouse) | File | ||
| trimming_adapters | File | |||
| trimming_adapter_trim_end | string | |||
| trimming_adapter_min_overlap | int | |||
| trimming_max_uncalled | int | |||
| trimming_min_readlength | int | |||
| kallisto_index | File | |||
| gene_transcript_lookup_table | File | |||
| strand | string? | |||
| refFlat | File | |||
| ribosomal_intervals | File | |||
| sample_name | string | |||
| unzip_fastqs | boolean? | |||
| examine_coding_effect | boolean? | |||
| fusioninspector_mode | ['null', {'type': 'enum', 'symbols': ['inspect', 'validate']}] |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| final_bam | File | ['.bai'] | ||
| star_fusion_out | File | |||
| star_junction_out | File | |||
| star_fusion_log | File | |||
| star_fusion_predict | File | |||
| star_fusion_abridge | File | |||
| stringtie_transcript_gtf | File | |||
| stringtie_gene_expression_tsv | File | |||
| transcript_abundance_tsv | File | |||
| transcript_abundance_h5 | File | |||
| gene_abundance | File | |||
| metrics | File | |||
| chart | File | |||
| fusion_evidence | File | |||
| xenosplit_statistics | File | |||
| bamcoverage_bigwig | File | |||
| coding_region_effects | File? | |||
| fusioninspector_evidence | File[]? |
| Name | CWL Run |
|---|---|
| sequence_to_trimmed_fastq | subworkflows/sequence_to_trimmed_fastq.cwl |
| graft_star_align_fusion | tools/star_align_fusion.cwl |
| host_star_align_fusion | tools/star_align_fusion.cwl |
| xenosplit | tools/xenosplit.cwl |
| graftbam_to_fastq | subworkflows/sequence_to_trimmed_fastq.cwl |
| graftbam_star_align_fusion | tools/star_align_fusion.cwl |
| star_fusion_detect | tools/star_fusion_detect.cwl |
| kallisto | tools/kallisto.cwl |
| transcript_to_gene | tools/transcript_to_gene.cwl |
| sort_bam | tools/samtools_sort.cwl |
| mark_dup | tools/mark_duplicates_and_sort.cwl |
| index_bam | tools/index_bam.cwl |
| stringtie | tools/stringtie.cwl |
| generate_qc_metrics | tools/generate_qc_metrics.cwl |
| cgpbigwig_bamcoverage | tools/bam_to_bigwig.cwl |