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sofstam 2022-12-01 11:12:31 +01:00
parent 8067012c01
commit e5bb627402
4 changed files with 65 additions and 26 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.motus_ncbi_id ? "-p" : "", params.motus_use_ncbi_ids ? "-p" : "",
params.motus_read_counts ? "-c" : "", params.motus_output_type ? "-c" : "",
params.motus_mgc_counts ? "-M ${task.ext.prefix}.mgc" : "" params.motus_save_mgcreadcounts ? "-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
motus_mgc_counts = true motus_save_mgcreadcounts = true
motus_ncbi_id = true motus_use_ncbi_ids = true
motus_read_counts = true motus_output_type = 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
motus_mgc_counts = false motus_output_type = false
motus_ncbi_id = false motus_use_ncbi_ids = false
motus_read_counts = false motus_save_mgcreadcounts = false
// krona // krona
run_krona = false run_krona = false

73
nextflow_schema.json
View file

@ -10,7 +10,11 @@
"type": "object", "type": "object",
"fa_icon": "fas fa-terminal", "fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.", "description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "databases", "outdir"], "required": [
"input",
"databases",
"outdir"
],
"properties": { "properties": {
"input": { "input": {
"type": "string", "type": "string",
@ -59,7 +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"
@ -88,7 +95,10 @@
"shortread_qc_tool": { "shortread_qc_tool": {
"type": "string", "type": "string",
"default": "fastp", "default": "fastp",
"enum": ["fastp", "adapterremoval"], "enum": [
"fastp",
"adapterremoval"
],
"fa_icon": "fas fa-tools", "fa_icon": "fas fa-tools",
"description": "Specify which tool to use for short-read QC" "description": "Specify which tool to use for short-read QC"
}, },
@ -147,7 +157,11 @@
"shortread_complexityfilter_tool": { "shortread_complexityfilter_tool": {
"type": "string", "type": "string",
"default": "bbduk", "default": "bbduk",
"enum": ["bbduk", "prinseqplusplus", "fastp"], "enum": [
"bbduk",
"prinseqplusplus",
"fastp"
],
"fa_icon": "fas fa-hammer", "fa_icon": "fas fa-hammer",
"description": "Specify which tool to use for complexity filtering" "description": "Specify which tool to use for complexity filtering"
}, },
@ -181,7 +195,10 @@
"shortread_complexityfilter_prinseqplusplus_mode": { "shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string", "type": "string",
"default": "entropy", "default": "entropy",
"enum": ["entropy", "dust"], "enum": [
"entropy",
"dust"
],
"fa_icon": "fas fa-check-square", "fa_icon": "fas fa-check-square",
"description": "Specify the complexity filter mode for PRINSEQ++" "description": "Specify the complexity filter mode for PRINSEQ++"
}, },
@ -355,7 +372,15 @@
"diamond_output_format": { "diamond_output_format": {
"type": "string", "type": "string",
"default": "tsv", "default": "tsv",
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"], "enum": [
"blast",
"xml",
"txt",
"daa",
"sam",
"tsv",
"paf"
],
"fa_icon": "fas fa-file", "fa_icon": "fas fa-file",
"description": "Specify output format from DIAMOND profiling.", "description": "Specify output format from DIAMOND profiling.",
"help_text": "DIAMOND can produce output in a number of different formats, you can specify here which to produce.\n\nNote that DIAMOND can only produce one format at a time, and depending on which you pick, some downstream steps may not be executed. For example, selecting `daa` or `sam` will mean you will not get a tabular taxonomic profile as with the other tools.\n\nWill be overriden by `--diamond_save_reads.`\n\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`" "help_text": "DIAMOND can produce output in a number of different formats, you can specify here which to produce.\n\nNote that DIAMOND can only produce one format at a time, and depending on which you pick, some downstream steps may not be executed. For example, selecting `daa` or `sam` will mean you will not get a tabular taxonomic profile as with the other tools.\n\nWill be overriden by `--diamond_save_reads.`\n\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`"
@ -374,7 +399,14 @@
"kaiju_taxon_rank": { "kaiju_taxon_rank": {
"type": "string", "type": "string",
"default": "species", "default": "species",
"enum": ["phylum", "class", "order", "family", "genus", "species"], "enum": [
"phylum",
"class",
"order",
"family",
"genus",
"species"
],
"fa_icon": "fas fa-tag", "fa_icon": "fas fa-tag",
"description": "Specify taxonomic rank to be displayed in Kaiju taxon table", "description": "Specify taxonomic rank to be displayed in Kaiju taxon table",
"help_text": "Specify the taxonomic level(s) to be displayed in the resulting Kaiju taxon table, as generated by the kaiju2table helper tool.\n\nThis can be either a single level (e.g. `species`), or a comma separated list to display the full taxonomic path (e.g. `superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`" "help_text": "Specify the taxonomic level(s) to be displayed in the resulting Kaiju taxon table, as generated by the kaiju2table helper tool.\n\nThis can be either a single level (e.g. `species`), or a comma separated list to display the full taxonomic path (e.g. `superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`"
@ -441,17 +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"
}, },
"motus_mgc_counts": { "motus_use_ncbi_ids": {
"type": "boolean", "type": "string",
"description": "Save the mgc reads count." "default": "false"
}, },
"motus_ncbi_id": { "motus_save_mgcreadcounts": {
"type": "boolean", "type": "string",
"description": "Print NCBI id." "default": "false"
}, },
"motus_read_counts": { "motus_output_type": {
"type": "boolean", "type": "string",
"description": "Print result as counts instead of relative abundances." "default": "false"
} }
}, },
"fa_icon": "fas fa-align-center" "fa_icon": "fas fa-align-center"
@ -592,7 +624,14 @@
"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": {