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sofstam 2022-11-29 16:57:07 +01:00
parent e85c75dcba
commit 933b820c19
4 changed files with 20 additions and 27 deletions
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6
conf/modules.config
View file

@ -448,9 +448,9 @@ process {
withName: MOTUS_PROFILE { withName: MOTUS_PROFILE {
ext.args = { ext.args = {
[ [
params.save_ncbi_id ? "-p" : "", params.motus_ncbi_id ? "-p" : "",
params.save_read_counts ? "-c" : "", params.motus_read_counts ? "-c" : "",
params.save_mgc_counts ? "-M ${task.ext.prefix}.mgc" : "" params.motus_mgc_counts ? "-M ${task.ext.prefix}.mgc" : ""
].join(',').replaceAll(','," ") ].join(',').replaceAll(','," ")
} }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }

6
conf/test_motus.config
View file

@ -39,8 +39,8 @@ params {
run_centrifuge = false run_centrifuge = false
run_diamond = false run_diamond = false
run_motus = true run_motus = true
save_mgc_counts = true motus_mgc_counts = true
save_ncbi_id = true motus_ncbi_id = true
save_read_counts = true motus_read_counts = true
run_profile_standardisation = true run_profile_standardisation = true
} }

6
nextflow.config
View file

@ -140,9 +140,9 @@ params {
// mOTUs // mOTUs
run_motus = false run_motus = false
save_mgc_counts = false motus_mgc_counts = false
save_ncbi_id = false motus_ncbi_id = false
save_read_counts = false motus_read_counts = false
// krona // krona
run_krona = false run_krona = false

29
nextflow_schema.json
View file

@ -63,7 +63,10 @@
"preprocessing_qc_tool": { "preprocessing_qc_tool": {
"type": "string", "type": "string",
"default": "fastqc", "default": "fastqc",
"enum": ["fastqc", "falco"], "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.", "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", "description": "Specify the tool used for quality control of raw sequencing reads",
"fa_icon": "fas fa-tools" "fa_icon": "fas fa-tools"
@ -470,17 +473,17 @@
"fa_icon": "fas fa-toggle-on", "fa_icon": "fas fa-toggle-on",
"description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases" "description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
}, },
"save_mgc_counts": { "motus_mgc_counts": {
"type": "boolean", "type": "boolean",
"description": "Save the mgc reads count for mOTUs." "description": "Save the mgc reads count."
}, },
"save_read_counts": { "motus_ncbi_id": {
"type": "boolean", "type": "boolean",
"description": "Print mOTUs result as counts instead of relative abundances." "description": "Print NCBI id."
}, },
"save_ncbi_id": { "motus_read_counts": {
"type": "boolean", "type": "boolean",
"description": "Print NCBI taxonomic id for mOTUs." "description": "Print result as counts instead of relative abundances."
} }
}, },
"fa_icon": "fas fa-align-center" "fa_icon": "fas fa-align-center"
@ -653,16 +656,6 @@
"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.",
@ -791,4 +784,4 @@
"$ref": "#/definitions/reference_genome_options" "$ref": "#/definitions/reference_genome_options"
} }
] ]
} }