strict-syntax-health/lint_results/prints-help-results/spatialvi_help.txt at main · nf-core/strict-syntax-health · 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
$ NXF_SYNTAX_PARSER=v2 nextflow run . --help


 N E X T F L O W   ~  version 26.01.1-edge

Launching `./main.nf` [happy_wescoff]revision: 29c9b239a2


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/spatialvi 1.0dev
------------------------------------------------------
Typical pipeline command:

  nextflow run nf-core/spatialvi -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>

help message of that parameter will be printed.
or `--helpFull`.

Input/output options
  --input                          [string] Path to comma-separated file containing information about the samples in the experiment.
  --outdir                         [string] The output directory where the results will be saved. You have to use absolute paths to storage on
Cloud infrastructure.
  --email                          [string] Email address for completion summary.
  --multiqc_title                  [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Space Ranger options
  --spaceranger_probeset           [string] Location of Space Ranger probeset file.
  --spaceranger_reference          [string] Location of Space Ranger reference directory. May be packed as `tar.gz` file. [default:
https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gz]

Optional outputs
  --spaceranger_save_reference     [boolean] Save the extracted tar archive of the Space Ranger reference.
  --save_untar_output              [boolean] Save extracted tar archives of input data.

Analysis options
  --hd_bin_size                    [integer] Bin size for Visium HD data. Only used for Visium HD. Allowed values: 2, 8, 16.  (accepted: 2,
8, 16) [default: 8]
  --qc_min_counts                  [integer] The minimum number of UMIs needed in a spot for that spot to pass the filtering. [default: 500]

  --qc_min_genes                   [integer] The minimum number of expressed genes in a spot needed for that spot to pass the filtering.
[default: 250]
  --qc_min_spots                   [integer] The minimum number of spots in which a gene is expressed for that gene to pass the filtering.
[default: 1]
  --qc_mito_threshold              [number]  The maximum proportion of mitochondrial content that a spot is allowed to have to pass the
filtering. [default: 20]
  --qc_ribo_threshold              [number]  The minimum proportion of ribosomal content that a spot is needs to have to pass the filtering (no
filtering is done by default). [default: 0]
  --qc_hb_threshold                [number]  The maximum proportion of haemoglobin content that a spot is allowed to have to pass the filtering
(no filtering is done by default). [default: 100]
  --cluster_n_hvgs                 [integer] The number of top highly variable genes to use for the analyses. [default: 2000]
  --cluster_resolution             [number]  The resolution for the clustering of the spots. [default: 1]
  --svg_autocorr_method            [string]  The method to use for spatially variable gene autocorrelation.  (accepted: moran, geary)
[default: moran]
  --n_top_svgs                     [integer] The number of top spatially variable genes to plot. [default: 14]

Data aggregation options
  --merge_sdata                    [boolean] Merge per-sample SpatialData objects into one.
  --integrate_sdata                [boolean] Integrate per-sample SpatialData objects into one and output a integration report.
  --integration_cluster_resolution [number]  The resolution for the clustering of the spots after integration of samples. [default: 1]
  --integration_n_hvgs             [integer] Number of highly variable genes to use for integration of samples. [default: 2000]

Generic options
  --multiqc_methods_description    [string]          Custom MultiQC yaml file containing HTML including a methods description.
  --help                           [boolean, string] Display the help message.
  --help_full                      [boolean]         Display the full detailed help message.
  --show_hidden                    [boolean]         Display hidden parameters in the help message (only works when --help or --help_full are provided).

 !! Hiding 18 param(s), use the `--showHidden` parameter to show them !!
------------------------------------------------------

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/spatialvi/blob/master/CITATIONS.md