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https://github.com/MillironX/taxprofiler.git
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Finalise first pass of nextflow json documentation
This commit is contained in:
James Fellows Yates
parent
bdcae4f934
commit
acd0570b4a
1 changed files with 33 additions and 56 deletions
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@ -10,11 +10,7 @@
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"type": "object",
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"type": "object",
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"fa_icon": "fas fa-terminal",
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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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"description": "Define where the pipeline should find input data and save output data.",
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"required": [
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"required": ["input", "databases", "outdir"],
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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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"properties": {
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"input": {
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"input": {
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"type": "string",
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"type": "string",
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@ -84,10 +80,7 @@
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"shortread_qc_tool": {
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"shortread_qc_tool": {
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"type": "string",
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"type": "string",
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"default": "fastp",
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"default": "fastp",
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"enum": [
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"enum": ["fastp", "adapterremoval"],
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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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"fa_icon": "fas fa-tools",
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"description": "Specify which tool to use for short-read QC"
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"description": "Specify which tool to use for short-read QC"
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},
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},
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@ -140,11 +133,7 @@
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"shortread_complexityfilter_tool": {
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"shortread_complexityfilter_tool": {
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"type": "string",
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"type": "string",
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"default": "bbduk",
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"default": "bbduk",
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"enum": [
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"enum": ["bbduk", "prinseqplusplus", "fastp"],
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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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"fa_icon": "fas fa-hammer",
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"description": "Specify which tool to use for complexity filtering"
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"description": "Specify which tool to use for complexity filtering"
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},
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},
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@ -178,10 +167,7 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"type": "string",
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"default": "entropy",
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"default": "entropy",
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"enum": [
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"enum": ["entropy", "dust"],
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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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"fa_icon": "fas fa-check-square",
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"description": "Specify the complexity filter mode for PRINSEQ++"
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"description": "Specify the complexity filter mode for PRINSEQ++"
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},
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},
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@ -344,7 +330,8 @@
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"centrifuge_save_reads": {
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"centrifuge_save_reads": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"fa_icon": "fas fa-save",
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"description": "Turn on saving of Centrifuge-aligned reads"
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"description": "Turn on saving of Centrifuge-aligned reads",
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"help_text": "Save mapped (SAM, FASTQ) and unmapped (FASTQ) reads from alignment step of centrifuge in your output results directory.\n\n> Modifies tool parameter(s):\n> centrifuge: `--un-gz`, `--al-gz`, `--un-conc-gz`, `--al-conc-gz`, `--out-fmt`"
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},
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},
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"run_diamond": {
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"run_diamond": {
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"type": "boolean",
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"type": "boolean",
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@ -354,22 +341,16 @@
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"diamond_output_format": {
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"diamond_output_format": {
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"type": "string",
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"type": "string",
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"default": "tsv",
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"default": "tsv",
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"enum": [
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
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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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"fa_icon": "fas fa-file",
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"description": "Specify output format from DIAMOND profiling."
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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\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`"
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},
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},
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"diamond_save_reads": {
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"diamond_save_reads": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"fa_icon": "fas fa-save",
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"description": "Turn on saving of DIAMOND-aligned reads. Will override --diamond_output_format and no taxon tables will be generated"
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"description": "Turn on saving of DIAMOND-aligned reads. Will override --diamond_output_format and no taxon tables will be generated",
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"help_text": "Save aligned reads in SAM format from alignment step of DIAMOND in your output results directory.\n\nNote this explicitly overrides `--diamond_output_format` to produce the SAM file, and no taxon table will be generated.\n\n> Modifies tool parameter(s):\n> - DIAMOND: `--outfmt`"
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},
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},
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"run_kaiju": {
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"run_kaiju": {
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"type": "boolean",
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"type": "boolean",
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@ -379,16 +360,10 @@
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"kaiju_taxon_rank": {
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"kaiju_taxon_rank": {
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"type": "string",
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"type": "string",
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"default": "species",
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"default": "species",
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"enum": [
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"enum": ["phylum", "class", "order", "family", "genus", "species"],
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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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"fa_icon": "fas fa-tag",
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"description": "Specify taxonomic rank to be displayed in Kaiju taxon table"
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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. `-l superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`"
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},
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},
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"run_kraken2": {
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"run_kraken2": {
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"type": "boolean",
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"type": "boolean",
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@ -398,12 +373,14 @@
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"kraken2_save_reads": {
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"kraken2_save_reads": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"fa_icon": "fas fa-save",
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"description": "Turn on saving of Kraken2-aligned reads"
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"description": "Turn on saving of Kraken2-aligned reads",
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"help_text": "Save reads that do and do not have a taxonomic classification in your output results directory in FASTQ format.\n\n> Modifies tool parameter(s):\n> - kraken2: `--classified-out` and `--unclassified-out`"
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},
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},
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"kraken2_save_readclassification": {
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"kraken2_save_readclassification": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"fa_icon": "fas fa-save",
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"description": "Turn on saving of Kraken2 per-read taxonomic assignment file"
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"description": "Turn on saving of Kraken2 per-read taxonomic assignment file",
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"help_text": "Save a text file that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic taxonomic assignment that that read recieved.\n\n> Modifies tool parameter(s):\n> - kraken2: `--output`"
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},
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},
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"run_malt": {
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"run_malt": {
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"type": "boolean",
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"type": "boolean",
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@ -414,17 +391,20 @@
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"type": "string",
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"type": "string",
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"default": "BlastN",
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"default": "BlastN",
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"fa_icon": "fas fa-check-square",
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"fa_icon": "fas fa-check-square",
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"description": "Specify which MALT alignment mode to use"
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"description": "Specify which MALT alignment mode to use",
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"help_text": "Specify which version of MALT alignment to use.\n\nBlastN is generally recommended (nucleotide-nucleotide alignment), but particularly for very short reads (such as aDNA), whereas BlastX mode is similar to DIAMOND and will translate the nucleotide to amino acid sequences. Note each type of alignment mode requires different parameters during database construction. Refer to the MALT manual for more information.\n\n> Modifies tool parameter(s):\n> - malt-run: `-mode` "
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},
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},
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"malt_save_reads": {
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"malt_save_reads": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"fa_icon": "fas fa-save",
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"description": "Turn on saving of MALT-aligned reads"
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"description": "Turn on saving of MALT-aligned reads",
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"help_text": "Turns on saving of MALT aligned reads in SAM format.\n\nRequires `-a` to be specified in your database arguments (see `--databases`).\n\nNote the SAM format produce by MALT is not completely valid, and may not work with downstream tools."
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},
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},
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"malt_generate_megansummary": {
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"malt_generate_megansummary": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-save",
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"fa_icon": "fas fa-save",
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"description": "Turn on generation of MEGAN summary file from MALT results"
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"description": "Turn on generation of MEGAN summary file from MALT results",
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"help_text": "Turns on saving of MALT output in an additional MEGAN summary file (`.megan`) that can be loaded into the MEGAN metagenomic exploration tool.\n\nNote this file is generated not directly from MALT but rather then MEGAN utility script `rma2info`.\n\n> Modifies tool parameter(s):\n> - rma2info: `-es`"
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},
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},
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"run_metaphlan3": {
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"run_metaphlan3": {
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"type": "boolean",
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"type": "boolean",
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@ -448,23 +428,27 @@
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"run_profile_standardisation": {
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"run_profile_standardisation": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-toggle-on",
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"fa_icon": "fas fa-toggle-on",
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"description": "Turn on standardisation of taxon tables across profilers"
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"description": "Turn on standardisation of taxon tables across profilers",
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"help_text": "Turns on standardisation of output OTU tables across all tools, each into a TSV format following the following scheme:\n\n|TAXON | SAMPLE_A | SAMPLE_B |\n|-------------|----------------|-----------------|\n| taxon_a | 32 | 123 |\n| taxon_b | 1 | 5 |\n\nThis currently only is generated for mOTUs."
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},
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},
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"generate_biom_output": {
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"generate_biom_output": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-toggle-on",
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"fa_icon": "fas fa-toggle-on",
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"description": "Turn on generation of BIOM output (currently only applies to mOTUs)"
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"description": "Turn on generation of BIOM output (currently only applies to mOTUs)",
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"help_text": "Turn on the saving of the taxonomic output in BIOM format (`.biom`) in the results directory of your pipeline run, instead of the default TSV format.\n\nNote this file is from the output of the `motus merge` command.\n\n> Modifies tool parameter(s):\n> - `-B -o`"
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},
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},
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"run_krona": {
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"run_krona": {
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"type": "boolean",
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"type": "boolean",
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"fa_icon": "fas fa-toggle-on",
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"fa_icon": "fas fa-toggle-on",
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"description": "Turn on generation of Krona plots for supported profilers"
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"description": "Turn on generation of Krona plots for supported profilers",
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"help_text": "Turn on the generation of Krona interactive pie-chart HTMLs for a selection of profilers.\n\nThe tools currently supported are:\n\n- centrifuge\n- kraken2\n- kaiju\n- MALT"
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},
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},
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"krona_taxonomy_directory": {
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"krona_taxonomy_directory": {
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"type": "string",
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"type": "string",
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"default": "None",
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"default": "None",
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"fa_icon": "fas fa-folder-open",
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"fa_icon": "fas fa-folder-open",
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"description": "Specify path to krona taxonomy directories (required for MALT krona plots)"
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"description": "Specify path to krona taxonomy directories (required for MALT krona plots)",
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"help_text": "Specify a path to a Krona taxonomy database directory (i.e. a directory containing a krona generated `.tab` file).\n\nThis is only required for generating Krona plots of MALT output.\n\nNote this taxonomy database must be downloaded and generated with the `updateTaxonomy.sh` script from the krona-tools package."
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}
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}
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},
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},
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"fa_icon": "fas fa-chart-line"
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"fa_icon": "fas fa-chart-line"
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@ -571,14 +555,7 @@
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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": [
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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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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