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sofstam
parent
8067012c01
commit
e5bb627402
4 changed files with 65 additions and 26 deletions
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@ -448,9 +448,9 @@ process {
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withName: MOTUS_PROFILE {
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ext.args = {
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[
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params.motus_ncbi_id ? "-p" : "",
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params.motus_read_counts ? "-c" : "",
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params.motus_mgc_counts ? "-M ${task.ext.prefix}.mgc" : ""
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params.motus_use_ncbi_ids ? "-p" : "",
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params.motus_output_type ? "-c" : "",
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params.motus_save_mgcreadcounts ? "-M ${task.ext.prefix}.mgc" : ""
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].join(',').replaceAll(','," ")
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}
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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@ -39,8 +39,8 @@ params {
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run_centrifuge = false
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run_diamond = false
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run_motus = true
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motus_mgc_counts = true
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motus_ncbi_id = true
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motus_read_counts = true
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motus_save_mgcreadcounts = true
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motus_use_ncbi_ids = true
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motus_output_type = true
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run_profile_standardisation = true
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}
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@ -140,9 +140,9 @@ params {
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// mOTUs
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run_motus = false
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motus_mgc_counts = false
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motus_ncbi_id = false
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motus_read_counts = false
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motus_output_type = false
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motus_use_ncbi_ids = false
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motus_save_mgcreadcounts = false
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// krona
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run_krona = false
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@ -10,7 +10,11 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "databases", "outdir"],
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"required": [
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"input",
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"databases",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -59,7 +63,10 @@
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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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"enum": [
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"fastqc",
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"falco"
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],
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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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"fa_icon": "fas fa-tools"
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@ -88,7 +95,10 @@
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"shortread_qc_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"],
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"enum": [
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"fastp",
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"adapterremoval"
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],
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"fa_icon": "fas fa-tools",
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"description": "Specify which tool to use for short-read QC"
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},
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@ -147,7 +157,11 @@
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk",
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"enum": ["bbduk", "prinseqplusplus", "fastp"],
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"enum": [
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"bbduk",
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"prinseqplusplus",
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"fastp"
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],
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"fa_icon": "fas fa-hammer",
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"description": "Specify which tool to use for complexity filtering"
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},
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@ -181,7 +195,10 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"],
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"enum": [
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"entropy",
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"dust"
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],
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"fa_icon": "fas fa-check-square",
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"description": "Specify the complexity filter mode for PRINSEQ++"
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},
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@ -355,7 +372,15 @@
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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],
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"fa_icon": "fas fa-file",
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"description": "Specify output format from DIAMOND profiling.",
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"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`"
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@ -374,7 +399,14 @@
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"kaiju_taxon_rank": {
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"type": "string",
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"default": "species",
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"enum": ["phylum", "class", "order", "family", "genus", "species"],
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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],
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"fa_icon": "fas fa-tag",
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"description": "Specify taxonomic rank to be displayed in Kaiju taxon table",
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"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`"
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@ -441,17 +473,17 @@
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"fa_icon": "fas fa-toggle-on",
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"description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
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},
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"motus_mgc_counts": {
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"type": "boolean",
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"description": "Save the mgc reads count."
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"motus_use_ncbi_ids": {
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"type": "string",
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"default": "false"
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},
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"motus_ncbi_id": {
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"type": "boolean",
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"description": "Print NCBI id."
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"motus_save_mgcreadcounts": {
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"type": "string",
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"default": "false"
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},
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"motus_read_counts": {
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"type": "boolean",
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"description": "Print result as counts instead of relative abundances."
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"motus_output_type": {
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"type": "string",
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"default": "false"
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}
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},
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"fa_icon": "fas fa-align-center"
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@ -592,7 +624,14 @@
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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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"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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},
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"email_on_fail": {
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