scrnaseq-standard.wdl

## scRNA-Seq Standard
##
## This WDL workflow runs the Cell Ranger scRNA-Seq alignment workflow for St. Jude Cloud.
##
## The workflow takes an input BAM file and splits it into FASTQ files for each read in the pair.
## The read pairs are then passed through Cell Ranger to generate a BAM file and perform
## quantification. Strandedness is inferred using ngsderive.
## File validation is performed at several steps, including immediately preceeding output.
##
## ## LICENSING
##
## #### MIT License
##
## Copyright 2022-Present St. Jude Children's Research Hospital
##
## Permission is hereby granted, free of charge, to any person obtaining a copy of this
## software and associated documentation files (the "Software"), to deal in the Software
## without restriction, including without limitation the rights to use, copy, modify, merge,
## publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons
## to whom the Software is furnished to do so, subject to the following conditions:
##
## The above copyright notice and this permission notice shall be included in all copies or
## substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
## BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
## DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
## OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

version 1.1

import "../../tools/cellranger.wdl"
import "../../tools/md5sum.wdl"
import "../../tools/ngsderive.wdl"
import "../../tools/picard.wdl"
import "../../tools/samtools.wdl"
import "./10x-bam-to-fastqs.wdl" as bam_to_fastqs

workflow scrnaseq_standard {
    parameter_meta {
        bam: "Input BAM format file to quality check"
        gtf: "Gzipped GTF feature file"
        transcriptome_tar_gz: "Database of reference files for Cell Ranger. Can be downloaded from 10x Genomics."
        prefix: "Prefix for output files"
        validate_input: "Ensure input BAM is well-formed before beginning harmonization?"
        use_all_cores: "Use all cores for multi-core steps?"
        subsample_n_reads: "Only process a random sampling of `n` reads. <=`0` for processing entire input BAM."
    }

    input {
        File bam
        File gtf
        File transcriptome_tar_gz
        String prefix = basename(bam, ".bam")
        Boolean validate_input = true
        Boolean use_all_cores = false
        Int subsample_n_reads = -1
    }

    if (validate_input) {
        call picard.validate_bam as validate_input_bam { input:
            bam=bam,
        }
    }

    if (subsample_n_reads > 0) {
        call samtools.subsample { input:
            bam=bam,
            desired_reads=subsample_n_reads,
            use_all_cores=use_all_cores,
        }
    }
    File selected_bam = select_first([subsample.sampled_bam, bam])

    call bam_to_fastqs.cell_ranger_bam_to_fastqs { input:
        bam=selected_bam,
        use_all_cores=use_all_cores,
    }

    call cellranger.count { input:
        fastqs_tar_gz=cell_ranger_bam_to_fastqs.fastqs_archive,
        transcriptome_tar_gz=transcriptome_tar_gz,
        id=prefix,
        use_all_cores=use_all_cores,
    }
    call picard.validate_bam { input: bam=count.bam }
    call ngsderive.strandedness { input:
        bam=count.bam,
        bam_index=count.bam_index,
        gene_model=gtf,
    }

    call md5sum.compute_checksum { input: file=count.bam }

    output {
        File harmonized_bam = count.bam
        File bam_checksum = compute_checksum.md5sum
        File bam_index = count.bam_index
        File qc = count.qc
        File barcodes = count.barcodes
        File features = count.features
        File matrix = count.matrix
        File filtered_gene_h5 = count.filtered_gene_h5
        File raw_gene_h5 = count.raw_gene_h5
        File raw_barcodes = count.raw_barcodes
        File raw_features = count.raw_features
        File raw_matrix = count.raw_matrix
        File mol_info_h5 = count.mol_info_h5
        File web_summary = count.web_summary
        File inferred_strandedness = strandedness.strandedness_file
    }
}