spatialaxe/main.nf at master · nf-core/spatialaxe · 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
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
#!/usr/bin/env nextflow
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    nf-core/spatialaxe
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Github : https://github.com/nf-core/spatialaxe
    Website: https://nf-co.re/spatialaxe
    Slack  : https://nfcore.slack.com/channels/spatialaxe
----------------------------------------------------------------------------------------
*/

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { SPATIALAXE               } from './workflows/spatialaxe.nf'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_spatialaxe_pipeline'
include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_spatialaxe_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// WORKFLOW: Run main analysis pipeline depending on type of input
//
workflow NFCORE_SPATIALAXE {

    take:
    samplesheet // channel: samplesheet read in from --input

    main:

    //
    // WORKFLOW: Run pipeline
    //
    SPATIALAXE (
        samplesheet,
        params.alignment_csv,
        params.baysor_config,
        params.baysor_prior,
        params.baysor_scale,
        params.baysor_tiling,
        params.baysor_tiling_scale,
        params.buffer_samples,
        params.buffer_size,
        params.cell_segmentation_only,
        params.cellpose_downscale,
        params.cellpose_model,
        params.expansion_distance,
        params.features,
        params.gene_panel,
        params.gene_synonyms,
        params.max_x,
        params.max_y,
        params.method,
        params.min_qv,
        params.min_x,
        params.min_y,
        params.mode,
        params.multiqc_config,
        params.multiqc_logo,
        params.multiqc_methods_description,
        params.nucleus_segmentation_only,
        params.offtarget_probe_tracking,
        params.outdir,
        params.probes_fasta,
        params.qupath_polygons,
        params.reference_annotations,
        params.relabel_genes,
        params.run_qc,
        params.segger_model,
        params.segmentation_mask,
        params.sharpen_tiff,
        params.stardist_nuclei_model,
        params.tiling,
        params.xeniumranger_only,
    )
    emit:
    multiqc_report = SPATIALAXE.out.multiqc_report // channel: /path/to/multiqc_report.html
}
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

    main:
    //
    // SUBWORKFLOW: Run initialisation tasks
    //
    PIPELINE_INITIALISATION (
        params.version,
        params.validate_params,
        params.monochrome_logs,
        args,
        params.outdir,
        params.input,
        params.help,
        params.help_full,
        params.show_hidden,
        params.format,
        params.gene_panel,
        params.gene_synonyms,
        params.image_seg_methods,
        params.method,
        params.mode,
        params.nucleus_segmentation_only,
        params.offtarget_probe_tracking,
        params.probes_fasta,
        params.reference_annotations,
        params.relabel_genes,
        params.segmentation_mask,
        params.transcript_seg_methods,
    )

    //
    // WORKFLOW: Run main workflow
    //
    NFCORE_SPATIALAXE (
        PIPELINE_INITIALISATION.out.samplesheet
    )
    //
    // SUBWORKFLOW: Run completion tasks
    //
    PIPELINE_COMPLETION (
        params.email,
        params.email_on_fail,
        params.plaintext_email,
        params.outdir,
        params.monochrome_logs,
        NFCORE_SPATIALAXE.out.multiqc_report
    )
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/