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This commit is contained in:
James Fellows Yates 2022-08-30 14:33:40 +02:00
parent d19a473c59
commit c2eaa3f6b0
1 changed files with 24 additions and 23 deletions
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nextflow_schema.json
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@ -74,7 +74,8 @@
"perform_shortread_qc": { "perform_shortread_qc": {
"type": "boolean", "type": "boolean",
"fa_icon": "fas fa-toggle-on", "fa_icon": "fas fa-toggle-on",
"description": "Turns on short read quality control steps (adapter clipping, complexity filtering etc.)" "description": "Turns on short read quality control steps (adapter clipping, complexity filtering etc.)",
"help_text": ""
}, },
"shortread_qc_tool": { "shortread_qc_tool": {
"type": "string", "type": "string",
@ -114,7 +115,7 @@
"type": "integer", "type": "integer",
"default": 15, "default": 15,
"fa_icon": "fas fa-ruler-horizontal", "fa_icon": "fas fa-ruler-horizontal",
"description": "Specify the minimum length of reads" "description": "Specify the minimum length of reads to be retained"
}, },
"perform_shortread_complexityfilter": { "perform_shortread_complexityfilter": {
"type": "boolean", "type": "boolean",
@ -183,33 +184,33 @@
"fa_icon": "fas fa-toggle-on", "fa_icon": "fas fa-toggle-on",
"description": "Turns on long read quality control steps (adapter clipping, length filtering etc.)" "description": "Turns on long read quality control steps (adapter clipping, length filtering etc.)"
}, },
"longread_qc_run_clip": { "longread_qc_skipadaptertrim": {
"type": "boolean", "type": "boolean",
"fa_icon": "fas fa-toggle-on", "description": "Skip long-read trimming",
"description": "Turn on long-read adapter clipping" "fa_icon": "fas fa-forward"
}, },
"longread_qc_run_filter": { "longread_qc_skipqualityfilter": {
"type": "boolean", "type": "boolean",
"fa_icon": "fas fa-toggle-on", "description": "Skip long-read length and quality filtering",
"description": "Turn on Filtlong long-read length filtering" "fa_icon": "fas fa-forward"
}, },
"longread_qc_keep_percent": { "longread_qc_qualityfilter_minlength": {
"type": "integer",
"default": 90,
"fa_icon": "fas fa-percent",
"description": "Specify minimum percentage of high-quality reads to keep during filtering"
},
"longread_qc_target_bases": {
"type": "integer",
"default": 500000000,
"fa_icon": "fas fa-bullseye",
"description": "Specify the target number of high-quality bases to retain overall during filtering"
},
"longread_qc_minlength": {
"type": "integer", "type": "integer",
"default": 1000, "default": 1000,
"fa_icon": "fas fa-ruler-horizontal", "description": "Specify the minimum length of reads to be retained",
"description": "Specify the minimum length of long-reads to retain during filtering" "fa_icon": "fas fa-ruler-horizontal"
},
"longread_qc_qualityfilter_keeppercent": {
"type": "integer",
"default": 90,
"description": "Specify the percent of high-quality reads to be retained",
"fa_icon": "fas fa-percentage"
},
"longread_qc_qualityfilter_targetbases": {
"type": "integer",
"default": 500000000,
"description": "Specify the minimum number of high-quality bases in the library to be retained",
"fa_icon": "fas fa-bullseye"
} }
}, },
"fa_icon": "fas fa-expand-alt" "fa_icon": "fas fa-expand-alt"