Kids First RNAseq Nextflow

This repo is currently a dev project of converting our CWL production workflow to Nextflow. Once development has complete, it will become a prod product.

Current State

The workflow is in alpha production shape. Currently, you cannot mix single and and paired end data with this workflow. In the test_inputs dir, there are examples of various input situations that have been tested. It can now run on CAVATICA, you can push this app by:

• Install sbpack
• Using command sbpack_nf --profile {your_profile} --appid {username}/{project}/kfdrc-rnaseq-nextflow --workflow-path /path/to/this/repo/Kids-First-RNAseq-Nextflow/ --entrypoint main.nf --sb-schema sb_nextflow_schema.yaml

Preprocess Reads Subworkflow:

The workflow takes in a mix of alignment files (BAM/CRAM) and fastq (single or paired end) and does the following:

Alignment input

1. Split by read group
2. Create STAR read group strings
3. Convert to FASTQ
4. Run cutadapt if a cutadapt-related param is given
5. Return an object with STAR RG strings and related fastqs for downstream processing

FASTQ input

1. Reformat to match object created by alignment input
2. Run cutadapt if a cutadapt-related param is given

Result

Return an object with STAR RG strings and related fastqs coming from the alignment input and/or fastq input for downstream processing and the added_metadata with the following:

• Paired end flag
• Read length median
• Read length std dev
• Strandedness

Align Analyze RNAseq

• STAR Align
• STAR Fusion
• Arriba Fusion
• T1K
• RNASeQC
• Kallisto

annoFuse Subworkflow

• Format Arriba
• Annotate Arriba
• Collate, filter, and annotate Arriba + Fusion results (annoFuse)

T1K Subworkflow

• Run T1K
• Filter results

DAGS

Main WF

flowchart TB
    subgraph " "
    subgraph params
    v6["read_length_median"]
    v16["sample_id"]
    v48["hla_rna_gene_coords"]
    v8["read_length_stddev"]
    v20["reference"]
    v2["input_fastq_reads"]
    v32["readFilesCommand"]
    v34["FusionGenome"]
    v38["assembly"]
    v24["output_basename"]
    v22["reference_index"]
    v18["threads"]
    v4["is_paired_end"]
    v44["RNAseQC_GTF"]
    v12["max_reads"]
    v14["line_filter"]
    v10["strandedness"]
    v30["genomeDir"]
    v46["hla_rna_ref_seqs"]
    v26["gtf_anno"]
    v40["samtools_threads"]
    v36["fusion_annotator_tar"]
    v28["kallisto_idx"]
    v42["RSEM_genome"]
    v0["input_alignment_reads"]
    end
    v50([preprocess_reads])
    v56([align_analyze_rnaseq])
    v57([annofuse_subworkflow])
    v58([rmats_subworkflow])
    v0 --> v50
    v2 --> v50
    v4 --> v50
    v6 --> v50
    v8 --> v50
    v10 --> v50
    v12 --> v50
    v14 --> v50
    v16 --> v50
    v18 --> v50
    v20 --> v50
    v26 --> v50
    v28 --> v50
    v32 --> v56
    v34 --> v56
    v40 --> v56
    v42 --> v56
    v44 --> v56
    v46 --> v56
    v16 --> v56
    v48 --> v56
    v50 --> v56
    v20 --> v56
    v22 --> v56
    v24 --> v56
    v26 --> v56
    v28 --> v56
    v30 --> v56
    v16 --> v57
    v36 --> v57
    v56 --> v57
    v24 --> v57
    v50 --> v58
    v56 --> v58
    v24 --> v58
    v26 --> v58
    end

Loading

Preprocess Reads

Align Analyze RNAseq

annoFuse Subworkflow

rMATS Subworkflow