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Fix merge conflic

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sofstam 2022-11-29 14:38:39 +01:00
parent 7e3ece53bd
commit f389029848
1 changed files with 741 additions and 734 deletions
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23
nextflow_schema.json
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@ -572,7 +572,14 @@
"description": "Method used to save pipeline results to output directory.", "description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy", "fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true "hidden": true
}, },
"email_on_fail": { "email_on_fail": {
@ -597,6 +604,13 @@
"fa_icon": "fas fa-file-upload", "fa_icon": "fas fa-file-upload",
"hidden": true "hidden": true
}, },
"preprocessing_qc_tool": {
"type": "string",
"default": "fastqc",
"enum": ["fastqc", "falco"],
"help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
"description": "Specify the tool used for quality control of raw sequencing reads"
},
"monochrome_logs": { "monochrome_logs": {
"type": "boolean", "type": "boolean",
"description": "Do not use coloured log outputs.", "description": "Do not use coloured log outputs.",
@ -726,13 +740,6 @@
} }
], ],
"properties": { "properties": {
"preprocessing_qc_tool": {
"type": "string",
"default": "fastqc",
"enum": ["fastqc", "falco"],
"help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
"description": "Specify the tool used for quality control of raw sequencing reads"
},
"save_mgc_counts": { "save_mgc_counts": {
"type": "boolean", "type": "boolean",
"description": "Save the mgc reads count for mOTUs." "description": "Save the mgc reads count for mOTUs."