eager/subworkflows/local/calculate_damage.nf at 5b1c505608ffcb1318bfb92eb21104da13e24340 · nf-core/eager · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
//
// Calculate damage profile
//

include { addNewMetaFromAttributes           } from '../../subworkflows/local/utils_nfcore_eager_pipeline/main'

include { DAMAGEPROFILER                     } from '../../modules/nf-core/damageprofiler/main'
include { MAPDAMAGE2 as CALCULATE_MAPDAMAGE2 } from '../../modules/nf-core/mapdamage2/main'

workflow CALCULATE_DAMAGE {
    take:
    ch_bam_bai //  [ [ meta ], [ bam ], [ bai ] ]
    fasta       // [ [ meta ], fasta ]
    fasta_fai   // [ [ meta ], fasta_fai ]

    main:
    ch_versions       = Channel.empty()
    ch_multiqc_files  = Channel.empty()

    //From deduplicate.nf
    ch_refs = fasta.join(fasta_fai)
        .map {
            // Prepend a new meta that contains the meta.id value as the new_meta.reference attribute
            addNewMetaFromAttributes( it, "id" , "reference" , false )
        }
    // Ensure input bam matches the regions file
    ch_damagetool_input = ch_bam_bai
        .map {
            // Prepend a new meta that contains the meta.reference value as the new_meta.reference attribute
            addNewMetaFromAttributes( it, "reference" , "reference" , false )
        }
        .combine(
                by:0,
                ch_refs
            )
            .multiMap{
                ignore_me, meta, bam, bai, meta2, fasta_, fasta_fai_ ->
                bam: [ meta, bam ]
                fasta: fasta_
                fasta_fai: fasta_fai_
            }
    // Calculate damage
    if ( params.damagecalculation_tool == 'damageprofiler' ) {
        DAMAGEPROFILER(
                ch_damagetool_input.bam,
                ch_damagetool_input.fasta,
                ch_damagetool_input.fasta_fai,
                []
            )
            ch_versions       = ch_versions.mix( DAMAGEPROFILER.out.versions.first() )
            ch_multiqc_files  = ch_multiqc_files.mix( DAMAGEPROFILER.out.results )
    } else if ( params.damagecalculation_tool == 'mapdamage' ) {
        CALCULATE_MAPDAMAGE2 ( ch_damagetool_input.bam, ch_damagetool_input.fasta )

        ch_versions      = ch_versions.mix( CALCULATE_MAPDAMAGE2.out.versions.first() )
        ch_multiqc_files = ch_multiqc_files.mix( CALCULATE_MAPDAMAGE2.out.folder )
    }

    emit:
    versions = ch_versions          // channel: [ versions.yml ]
    mqc      = ch_multiqc_files
}