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Merge pull request GlobalPneumoSeq#63 from HarryHung/feature/better-t…
…ower-support Proper Nextflow Tower Support Former-commit-id: ec1516c
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,288 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", | ||
| "title": "GPS Unified Pipeline Parameters", | ||
| "description": "", | ||
| "type": "object", | ||
| "definitions": { | ||
| "input_output": { | ||
| "title": "Input / Output", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "reads": { | ||
| "type": "string", | ||
| "description": "Path to the input directory that contains the reads to be processed." | ||
| }, | ||
| "output": { | ||
| "type": "string", | ||
| "description": "Path to the output directory that save the results." | ||
| }, | ||
| "assembly_publish": { | ||
| "type": "string", | ||
| "description": "Method used by Nextflow to publish the generated assemblies.", | ||
| "hidden": true | ||
| } | ||
| }, | ||
| "required": [ | ||
| "reads", | ||
| "output", | ||
| "assembly_publish" | ||
| ] | ||
| }, | ||
| "qc_parameters": { | ||
| "title": "QC Parameters", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "spneumo_percentage": { | ||
| "type": "number", | ||
| "description": "Minimum S. pneumoniae percentage in reads to pass Taxonomy QC.", | ||
| "hidden": true | ||
| }, | ||
| "ref_coverage": { | ||
| "type": "number", | ||
| "description": "Minimum reference coverage percentage by the reads to pass Mapping QC.", | ||
| "hidden": true | ||
| }, | ||
| "het_snp_site": { | ||
| "type": "integer", | ||
| "description": "Maximum non-cluster heterozygous SNP (Het-SNP) site count to pass Mapping QC.", | ||
| "hidden": true | ||
| }, | ||
| "contigs": { | ||
| "type": "integer", | ||
| "hidden": true, | ||
| "description": "Maximum contig count in assembly to pass Assembly QC." | ||
| }, | ||
| "length_low": { | ||
| "type": "integer", | ||
| "hidden": true, | ||
| "description": "Minimum assembly length to pass Assembly QC." | ||
| }, | ||
| "length_high": { | ||
| "type": "integer", | ||
| "hidden": true, | ||
| "description": "Maximum assembly length to pass Assembly QC." | ||
| }, | ||
| "depth": { | ||
| "type": "number", | ||
| "hidden": true, | ||
| "description": "Minimum sequencing depth to pass Assembly QC." | ||
| } | ||
| }, | ||
| "required": [ | ||
| "spneumo_percentage", | ||
| "ref_coverage", | ||
| "het_snp_site", | ||
| "contigs", | ||
| "length_low", | ||
| "length_high", | ||
| "depth" | ||
| ] | ||
| }, | ||
| "assembly": { | ||
| "title": "Assembly", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "assembler": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Using which SPAdes-based assembler to assemble the reads." | ||
| }, | ||
| "min_contig_length": { | ||
| "type": "integer", | ||
| "description": "Minimum legnth of contig to be included in the assembly.", | ||
| "hidden": true | ||
| } | ||
| }, | ||
| "required": [ | ||
| "assembler", | ||
| "min_contig_length" | ||
| ] | ||
| }, | ||
| "mapping": { | ||
| "title": "Mapping", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "ref_genome": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Path to the reference genome for mapping." | ||
| }, | ||
| "ref_genome_bwa_db_local": { | ||
| "type": "string", | ||
| "description": "Path to the directory where the reference genome FM-index database for BWA should be saved to.", | ||
| "hidden": true | ||
| } | ||
| }, | ||
| "required": [ | ||
| "ref_genome", | ||
| "ref_genome_bwa_db_local" | ||
| ] | ||
| }, | ||
| "taxonomy": { | ||
| "title": "Taxonomy", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "kraken2_db_remote": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "URL to a Kraken2 database." | ||
| }, | ||
| "kraken2_db_local": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Path to the directory where the remote Kraken2 database should be saved to." | ||
| }, | ||
| "kraken2_memory_mapping": { | ||
| "type": "boolean", | ||
| "hidden": true, | ||
| "description": "Using the memory mapping option of Kraken2 or not." | ||
| } | ||
| }, | ||
| "required": [ | ||
| "kraken2_db_remote", | ||
| "kraken2_db_local", | ||
| "kraken2_memory_mapping" | ||
| ] | ||
| }, | ||
| "serotype": { | ||
| "title": "Serotype", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "seroba_db_remote": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "URL to a SeroBA Git remote repository." | ||
| }, | ||
| "seroba_db_local": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Path to the directory where SeroBA local repository should be saved to." | ||
| }, | ||
| "seroba_kmer": { | ||
| "type": "integer", | ||
| "hidden": true, | ||
| "description": "Kmer size for creating the KMC database of SeroBA." | ||
| } | ||
| }, | ||
| "required": [ | ||
| "seroba_db_remote", | ||
| "seroba_db_local", | ||
| "seroba_kmer" | ||
| ] | ||
| }, | ||
| "lineage": { | ||
| "title": "Lineage", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "poppunk_db_remote": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "URL to a PopPUNK database." | ||
| }, | ||
| "poppunk_ext_remote": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "URL to a PopPUNK external clusters file." | ||
| }, | ||
| "poppunk_db_local": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Path to the directory where the remote PopPUNK database and external clusters file should be saved to." | ||
| } | ||
| }, | ||
| "required": [ | ||
| "poppunk_db_remote", | ||
| "poppunk_ext_remote", | ||
| "poppunk_db_local" | ||
| ] | ||
| }, | ||
| "other_amr": { | ||
| "title": "Other AMR", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "ariba_ref": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Path to the reference sequences for ARIBA." | ||
| }, | ||
| "ariba_metadata": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Path to the metadata file for ARIBA." | ||
| }, | ||
| "ariba_db_local": { | ||
| "type": "string", | ||
| "hidden": true, | ||
| "description": "Path to the directory where ARIBA reference database should be saved to." | ||
| } | ||
| }, | ||
| "required": [ | ||
| "ariba_ref", | ||
| "ariba_metadata", | ||
| "ariba_db_local" | ||
| ] | ||
| }, | ||
| "singularity": { | ||
| "title": "Singularity", | ||
| "type": "object", | ||
| "description": "", | ||
| "default": "", | ||
| "properties": { | ||
| "singularity_cachedir": { | ||
| "type": "string", | ||
| "description": "Path to the directory where Singularity images should be saved to.", | ||
| "hidden": true | ||
| } | ||
| }, | ||
| "required": [ | ||
| "singularity_cachedir" | ||
| ] | ||
| } | ||
| }, | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/input_output" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/qc_parameters" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/assembly" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/mapping" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/taxonomy" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/serotype" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/lineage" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/other_amr" | ||
| }, | ||
| { | ||
| "$ref": "#/definitions/singularity" | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| reports: | ||
| results.csv: | ||
| display: "Overall Results" |