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Fix merge conflic
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7e3ece53bd
commit
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1 changed files with 741 additions and 734 deletions
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@ -572,7 +572,14 @@
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"description": "Method used to save pipeline results to output directory.",
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"description": "Method used to save pipeline results to output directory.",
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"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.",
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"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.",
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"fa_icon": "fas fa-copy",
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"fa_icon": "fas fa-copy",
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"hidden": true
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"hidden": true
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},
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},
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"email_on_fail": {
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"email_on_fail": {
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@ -597,6 +604,13 @@
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"fa_icon": "fas fa-file-upload",
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"fa_icon": "fas fa-file-upload",
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"hidden": true
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"hidden": true
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},
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},
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"preprocessing_qc_tool": {
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"type": "string",
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"default": "fastqc",
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"enum": ["fastqc", "falco"],
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"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.",
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"description": "Specify the tool used for quality control of raw sequencing reads"
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},
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"monochrome_logs": {
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"monochrome_logs": {
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"type": "boolean",
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"type": "boolean",
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"description": "Do not use coloured log outputs.",
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"description": "Do not use coloured log outputs.",
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@ -726,13 +740,6 @@
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}
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}
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],
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],
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"properties": {
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"properties": {
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"preprocessing_qc_tool": {
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"type": "string",
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"default": "fastqc",
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"enum": ["fastqc", "falco"],
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"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.",
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"description": "Specify the tool used for quality control of raw sequencing reads"
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},
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"save_mgc_counts": {
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"save_mgc_counts": {
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"type": "boolean",
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"type": "boolean",
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"description": "Save the mgc reads count for mOTUs."
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"description": "Save the mgc reads count for mOTUs."
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