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Don't double-mention default values in the schema
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Co-authored-by: Thiseas C. Lamnidis <[email protected]>
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@jch-13 @TCLamnidis
jch-13 and TCLamnidis authored Oct 7, 2024
1 parent 4e48a35 commit d5fd7f0
Showing 1 changed file with 10 additions and 10 deletions.
20 changes: 10 additions & 10 deletions nextflow_schema.json
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"type": "number",
"default": 0.5,
"description": "Specify the -f parameter for mapAD, which sets the 5'-overhang length parameter of mapAD's aDNA scoring model.",
"help_text": "Configures mapAD's 5' single-stranded overhang length parameter. Increased cytosine deamination rates are expected in single-stranded overhangs resulting from aDNA damage. The `-l` parameter adjusts the probability with which the scoring model expects a position in the read to be in a single-stranded overhang at the 5'-end (pos^`-f`). Default is set to 0.5.\n\n> Modifies mapAD map parameter: `-f`",
"help_text": "Configures mapAD's 5' single-stranded overhang length parameter. Increased cytosine deamination rates are expected in single-stranded overhangs resulting from aDNA damage. The `-l` parameter adjusts the probability with which the scoring model expects a position in the read to be in a single-stranded overhang at the 5'-end (pos^`-f`).\n\n> Modifies mapAD map parameter: `-f`",
"fa_icon": "fas fa-long-arrow-alt-left"
},
"mapping_mapad_t": {
"type": "number",
"default": 0.5,
"description": "Specify the -t parameter for mapAD, which sets the 3'-overhang length parameter of mapAD's aDNA scoring model.",
"help_text": "Configures mapAD's 3' single-stranded overhang length parameter. Increased cytosine deamination rates are expected in single-stranded overhangs resulting from aDNA damage. The `-t` parameter adjusts the probability with which the scoring model expects a position in the read to be in a single-stranded overhang at the 3'-end (pos^`-t`). Default is set to 0.5.\n\n> Modifies mapAD map parameter: `-t`",
"help_text": "Configures mapAD's 3' single-stranded overhang length parameter. Increased cytosine deamination rates are expected in single-stranded overhangs resulting from aDNA damage. The `-t` parameter adjusts the probability with which the scoring model expects a position in the read to be in a single-stranded overhang at the 3'-end (pos^`-t`).\n\n> Modifies mapAD map parameter: `-t`",
"fa_icon": "fas fa-long-arrow-alt-right"
},
"mapping_mapad_d": {
"type": "number",
"default": 0.02,
"description": "Specify the -d parameter for mapAD, which sets the double-stranded deamination rate parameter of mapAD's aDNA scoring model.",
"help_text": "Configures mapAD's double-stranded deamination rate parameter. The `-d` parameter adjusts the expected deamination rate in double-stranded central \"stems\" of aDNA fragments. Default is set to 0.02.\n\n> Modifies mapAD map parameter: `-d`",
"help_text": "Configures mapAD's double-stranded deamination rate parameter. The `-d` parameter adjusts the expected deamination rate in double-stranded central \"stems\" of aDNA fragments.\n\n> Modifies mapAD map parameter: `-d`",
"fa_icon": "fas fa-equals"
},
"mapping_mapad_s": {
"type": "number",
"default": 1,
"description": "Specify the -s parameter for mapAD, which sets the single-stranded deamination rate parameter of mapAD's aDNA scoring model.",
"help_text": "Configures mapAD's single-stranded deamination rate parameter. The `-s` parameter adjusts the expected deamination rate in single-stranded overhangs of aDNA fragments (whose lengths are modeled via the `-f` and `-t` parameters). Default is set to 1.0.\n\n> Modifies mapAD map parameter: `-s`",
"help_text": "Configures mapAD's single-stranded deamination rate parameter. The `-s` parameter adjusts the expected deamination rate in single-stranded overhangs of aDNA fragments (whose lengths are modeled via the `-f` and `-t` parameters).\n\n> Modifies mapAD map parameter: `-s`",
"fa_icon": "fas fa-minus"
},
"mapping_mapad_i": {
"type": "number",
"default": 0.001,
"description": "Specify the -i parameter for mapAD, which adjusts the expected indel rate between reads and reference.",
"help_text": "Configures mapAD's expected InDel rate parameter. The `-i` parameter adjusts the gap open penalty of mapAD's affine gap model. Default is set to 0.001.\n\n> Modifies mapAD map parameter: `-i`",
"help_text": "Configures mapAD's expected InDel rate parameter. The `-i` parameter adjusts the gap open penalty of mapAD's affine gap model.\n\n> Modifies mapAD map parameter: `-i`",
"fa_icon": "fas fa-ellipsis-h"
},
"mapping_mapad_x": {
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"type": "number",
"default": 5,
"description": "Specify the --gap_dist_ends parameter for mapAD, which defines the distance from the read ends in which no gaps are permitted.",
"help_text": "Configures mapAD's `--gap_dist_ends` parameter which defines the distance from the read ends in which no gaps are permitted. Default is set to mapAD's default (5).\n\n> Modifies mapAD map parameter: `--gap_dist_ends`",
"help_text": "Configures mapAD's `--gap_dist_ends` parameter which defines the distance from the read ends in which no gaps are permitted.\n\n> Modifies mapAD map parameter: `--gap_dist_ends`",
"fa_icon": "fas fa-step-forward"
},
"mapping_mapad_maxnumopengaps": {
"type": "number",
"default": 2,
"description": "Specify the number of gaps allowed for alignment with mapAD.",
"help_text": "Specify the number of gaps allowed for mapping with mapAD. Default is set to mapAD's default (2).\n\n> Modifies mapAD map parameter: `--max_num_gaps_open`",
"help_text": "Specify the number of gaps allowed for mapping with mapAD.\n\n> Modifies mapAD map parameter: `--max_num_gaps_open`",
"fa_icon": "fas fa-people-arrows"
},
"mapping_mapad_baseerrorrate": {
"type": "number",
"default": 0.02,
"description": "Specify the base error rate parameter for mapAD.",
"help_text": "Configures mapAD's base error rate parameter. The `-D` parameter adjusts the base error rate which is one of the underlying parts of mapAD's scoring model. Should not normally need to be adjusted. Default is set to mapAD's default (0.02).\n\n> Modifies mapAD map parameter: `-D`",
"help_text": "Configures mapAD's base error rate parameter. The `-D` parameter adjusts the base error rate which is one of the underlying parts of mapAD's scoring model. Should not normally need to be adjusted.\n\n> Modifies mapAD map parameter: `-D`",
"fa_icon": "fas fa-percentage"
},
"mapping_mapad_ignorebasequal": {
"type": "boolean",
"description": "Set the --ignore_base_quality flag, which instructs mapAD to ignore base quality values in its scoring model.",
"help_text": "Without this flag, mapAD is more permissive in terms of mismatches if the quality of the base is low. Default is set to mapAD's default.\n\n> Modifies mapAD map parameter: `--ignore_base_quality`",
"help_text": "Without this flag, mapAD is more permissive in terms of mismatches if the quality of the base is low.\n\n> Modifies mapAD map parameter: `--ignore_base_quality`",
"fa_icon": "fas fa-asterisk"
},
"mapping_mapad_stacklimitabort": {
"type": "boolean",
"description": "Set the --stack_limit_abort flag, which instructs mapAD to not try and recover from a full backtracking stack.",
"help_text": "Without this flag, mapAD tries to recover from a full backtracking stack by removing low-scoring sub-alignments. This can help to recover from difficult to map reads, at the cost of a slower alignment. Setting this flag will speed up the alignment process. Default is set to mapAD's default.\n\n> Modifies mapAD map parameter: `--stack_limit_abort`",
"help_text": "Without this flag, mapAD tries to recover from a full backtracking stack by removing low-scoring sub-alignments. This can help to recover from difficult to map reads, at the cost of a slower alignment. Setting this flag will speed up the alignment process.\n\n> Modifies mapAD map parameter: `--stack_limit_abort`",
"fa_icon": "fab fa-stack-overflow"
}
},
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