From e5bb627402179b42ef817845db8c99a0546c4a16 Mon Sep 17 00:00:00 2001 From: sofstam Date: Thu, 1 Dec 2022 11:12:31 +0100 Subject: [PATCH] Apply review suggestions --- conf/modules.config | 6 ++-- conf/test_motus.config | 6 ++-- nextflow.config | 6 ++-- nextflow_schema.json | 73 ++++++++++++++++++++++++++++++++---------- 4 files changed, 65 insertions(+), 26 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 63be9ff..1ff6f55 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -448,9 +448,9 @@ process { withName: MOTUS_PROFILE { ext.args = { [ - params.motus_ncbi_id ? "-p" : "", - params.motus_read_counts ? "-c" : "", - params.motus_mgc_counts ? "-M ${task.ext.prefix}.mgc" : "" + params.motus_use_ncbi_ids ? "-p" : "", + params.motus_output_type ? "-c" : "", + params.motus_save_mgcreadcounts ? "-M ${task.ext.prefix}.mgc" : "" ].join(',').replaceAll(','," ") } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } diff --git a/conf/test_motus.config b/conf/test_motus.config index 8eb324b..b5c2c51 100644 --- a/conf/test_motus.config +++ b/conf/test_motus.config @@ -39,8 +39,8 @@ params { run_centrifuge = false run_diamond = false run_motus = true - motus_mgc_counts = true - motus_ncbi_id = true - motus_read_counts = true + motus_save_mgcreadcounts = true + motus_use_ncbi_ids = true + motus_output_type = true run_profile_standardisation = true } diff --git a/nextflow.config b/nextflow.config index c9bb0f4..b1da76a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -140,9 +140,9 @@ params { // mOTUs run_motus = false - motus_mgc_counts = false - motus_ncbi_id = false - motus_read_counts = false + motus_output_type = false + motus_use_ncbi_ids = false + motus_save_mgcreadcounts = false // krona run_krona = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 2fcdd80..7c4998a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,7 +10,11 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["input", "databases", "outdir"], + "required": [ + "input", + "databases", + "outdir" + ], "properties": { "input": { "type": "string", @@ -59,7 +63,10 @@ "preprocessing_qc_tool": { "type": "string", "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.", "description": "Specify the tool used for quality control of raw sequencing reads", "fa_icon": "fas fa-tools" @@ -88,7 +95,10 @@ "shortread_qc_tool": { "type": "string", "default": "fastp", - "enum": ["fastp", "adapterremoval"], + "enum": [ + "fastp", + "adapterremoval" + ], "fa_icon": "fas fa-tools", "description": "Specify which tool to use for short-read QC" }, @@ -147,7 +157,11 @@ "shortread_complexityfilter_tool": { "type": "string", "default": "bbduk", - "enum": ["bbduk", "prinseqplusplus", "fastp"], + "enum": [ + "bbduk", + "prinseqplusplus", + "fastp" + ], "fa_icon": "fas fa-hammer", "description": "Specify which tool to use for complexity filtering" }, @@ -181,7 +195,10 @@ "shortread_complexityfilter_prinseqplusplus_mode": { "type": "string", "default": "entropy", - "enum": ["entropy", "dust"], + "enum": [ + "entropy", + "dust" + ], "fa_icon": "fas fa-check-square", "description": "Specify the complexity filter mode for PRINSEQ++" }, @@ -355,7 +372,15 @@ "diamond_output_format": { "type": "string", "default": "tsv", - "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"], + "enum": [ + "blast", + "xml", + "txt", + "daa", + "sam", + "tsv", + "paf" + ], "fa_icon": "fas fa-file", "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`" @@ -374,7 +399,14 @@ "kaiju_taxon_rank": { "type": "string", "default": "species", - "enum": ["phylum", "class", "order", "family", "genus", "species"], + "enum": [ + "phylum", + "class", + "order", + "family", + "genus", + "species" + ], "fa_icon": "fas fa-tag", "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`" @@ -441,17 +473,17 @@ "fa_icon": "fas fa-toggle-on", "description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases" }, - "motus_mgc_counts": { - "type": "boolean", - "description": "Save the mgc reads count." + "motus_use_ncbi_ids": { + "type": "string", + "default": "false" }, - "motus_ncbi_id": { - "type": "boolean", - "description": "Print NCBI id." + "motus_save_mgcreadcounts": { + "type": "string", + "default": "false" }, - "motus_read_counts": { - "type": "boolean", - "description": "Print result as counts instead of relative abundances." + "motus_output_type": { + "type": "string", + "default": "false" } }, "fa_icon": "fas fa-align-center" @@ -592,7 +624,14 @@ "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.", "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], "hidden": true }, "email_on_fail": {