name: "fastq_align_chromap"
description: Align high throughput chromatin profiles using Chromap then sort with samtools
keywords:
  - align
  - fasta
  - genome
  - reference
  - chromatin profiles
  - chip-seq
  - atac-seq
  - hic
modules:
  - chromap/chromap
  - samtools/sort
  - samtools/index
  - samtools/stats
  - samtools/idxstats
  - samtools/flagstat
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - ch_reads:
      type: file
      description: |
        Structure: [val(meta), path(reads)]
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - ch_index:
      type: file
      description: |
        Structure: [val(meta2), path(index)]
        Chromap genome index files
      pattern: "*.index"
  - ch_fasta:
      type: file
      description: |
        Structure: [val(meta2), path(fasta)]
        Reference fasta file
      pattern: "*.{fasta,fa}"
  - ch_barcodes:
      type: file
      description: |
        Structure: [path(barcodes)]
        Cell barcode files
  - ch_whitelist:
      type: file
      description: |
        Structure: [path(whitelist)]
        Cell barcode whitelist file
  - ch_chr_order:
      type: file
      description: |
        Structure: [path(chr_order)]
        Custom chromosome order
  - ch_pairs_chr_order:
      type: file
      description: |
        Structure: [path(pairs_chr_order)]
        Natural chromosome order for pairs flipping
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bam:
      type: file
      description: BAM file
      pattern: "*.bam"
  - bai:
      type: file
      description: BAM index (currently only for snapaligner)
      pattern: "*.bai"
  - stats:
      type: file
      description: File containing samtools stats output
      pattern: "*.{stats}"
  - flagstat:
      type: file
      description: File containing samtools flagstat output
      pattern: "*.{flagstat}"
  - idxstats:
      type: file
      description: File containing samtools idxstats output
      pattern: "*.{idxstats}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@JoseEspinosa"
