fastq_align_chromap

Align high throughput chromatin profiles using Chromap, updating readgroups if neccessary and then sort with samtools

alignfastagenomereferencechromatin profileschip-seqatac-seqhic

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fastq_align_chromap

Description

Align high throughput chromatin profiles using Chromap, updating readgroups if neccessary and then sort with samtools

Input

name

description

pattern

`ch_reads`

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. The meta map contains sample information,
e.g. [ id:‘test’, single_end:false ].

Structure: [ val(meta), [ path(reads) ] ]

`ch_index`

Chromap genome index files. The meta map contains reference information,
e.g. [ id:‘test’ ].

Structure: [ val(meta2), path(index) ]

*.index

`ch_fasta_fai`

Reference fasta file and index.

Structure: [ val(meta2), path(fasta), path(fai) ]

`ch_barcodes`

Cell barcode files.

Structure: [ path(barcodes) ]

`ch_whitelist`

Cell barcode whitelist file.

Structure: [ path(whitelist) ]

`ch_chr_order`

Custom chromosome order.

Structure: [ path(chr_order) ]

`ch_pairs_chr_order`

Natural chromosome order for pairs flipping.

Structure: [ path(pairs_chr_order) ]

`update_readgroups`

Boolean controling whether the readgroups should be added or updated
after chromap alignment

Output

name

description

pattern

`bam`

Sorted BAM file.

Structure: [ val(meta), path(bam) ]

*.bam

`index`

BAM index.

Structure: [ val(meta), path(index) ]

*.{bai,csi}

`stats`

File containing samtools stats output.

Structure: [ val(meta), path(stats) ]

*.stats

`flagstat`

File containing samtools flagstat output.

Structure: [ val(meta), path(flagstat) ]

*.flagstat

`idxstats`

File containing samtools idxstats output.

Structure: [ val(meta), path(idxstats) ]

*.idxstats