strict-syntax-health/lint_results/prints-help-results/proteinannotator_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
81
82
83
84
85
86
87
88
$ NXF_SYNTAX_PARSER=v2 nextflow run . --help


 N E X T F L O W   ~  version 26.02.0-edge

Downloading plugin nf-schema@2.6.1
Launching `./main.nf` [astonishing_chandrasekhar] revision: 0c5aca65cf


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/proteinannotator 1.1.0dev
------------------------------------------------------
Typical pipeline command:

  nextflow run nf-core/proteinannotator -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.

Generic options
  --multiqc_methods_description   [string]          Custom MultiQC yaml file containing HTML including a methods description.
  --modules_testdata_base_path    [string]          Base URL or local path to location of modules test dataset files
  --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).


Quality check parameters
  --skip_preprocessing            [boolean] Skip all default QC steps for sequences (gap trimming, length filtering, validation, duplicate
removal).
  --min_seq_length                [integer] The minimum allowed sequence length [default: 30]
  --max_seq_length                [integer] The maximum allowed sequence length [default: 5000]
  --remove_duplicates_on_sequence [boolean] Remove duplicate input amino acid sequences, based on the sequence.

Domain annotation parameters
  --skip_pfam                     [boolean] Skip the domain annotation with the Pfam database.
  --pfam_db                       [string]  Path to an already installed Pfam HMM database (.hmm.gz).
  --pfam_latest_link              [string]  InterPro hosted link to the latest Pfam HMM database file. [default:
https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz]
  --skip_funfam                   [boolean] Skip the domain annotation with the FunFam database.
  --funfam_db                     [string]  Path to an already installed FunFam HMM database (.lib.gz).
  --funfam_latest_link            [string]  CATH hosted link to the latest available (v4_3_0) FunFam HMM database file. [default:
https://download.cathdb.info/cath/releases/all-releases/v4_3_0/sequence-data/funfam-hmm3-v4_3_0.lib.gz]

  --skip_nmpfams                  [boolean] Skip the domain annotation with the NMPFams database.
  --nmpfams_db                    [string]  Path to an already installed NMPFams HMM database.
  --nmpfams_latest_link           [string]  [default: https://pavlopoulos-lab.org/envofams/databases/hmmer/nmpfamsdb.hmm.gz]
  --hmmsearch_evalue_cutoff       [number]  hmmsearch e-value cutoff threshold for reported results. Modifies the -E parameter of hmmsearch.
[default: 0.001]

Functional annotation parameters
  --skip_interproscan             [boolean] Run InterProScan [default: false]
  --interproscan_db_url           [string]  Change the database version used for annotation. [default:
https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.72-103.0/interproscan-5.72-103.0-64-bit.tar.gz]

  --interproscan_db               [string]  Path to pre-downloaded InterProScan database.
  --interproscan_applications     [string]  Assigns the database(s) to be used to annotate the coding regions. [default:
Hamap,PANTHER,PIRSF,TIGRFAM,sfld]
  --interproscan_enableprecalc    [boolean] Pre-calculates residue mutual matches.

Prediction parameters
  --skip_s4pred                   [boolean] Skip the secondary structure prediction.
  --s4pred_outfmt                 [string]  Choose the output format (i.e., 'ss2', 'fas', 'horiz') for the s4pred per amino acid probability
predictions (i.e., α-helix, β-strand, coil). Modifies the --outfmt parameter of s4pred run_model.
 (accepted: ss2, fas, horiz) [default: ss2]
 !! Hiding 18 param(s), use the `--showHidden` parameter to show them !!
------------------------------------------------------

* The pipeline
    https://doi.org/10.5281/zenodo.18547735

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

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