mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 20:43:09 +00:00
Fix adapterremoval adapter conflict and add optional adapter list file
This commit is contained in:
parent
63c260bfbc
commit
76a662ecc5
8 changed files with 69 additions and 24 deletions
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@ -100,8 +100,7 @@ process {
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withName: ADAPTERREMOVAL_SINGLE {
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ext.args = [
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
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params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
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params.shortread_qc_skipadaptertrim ? "--adapter1 ''" : params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
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// filtering options
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"--minlength ${params.shortread_qc_minlength}"
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].join(' ').trim()
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@ -119,9 +118,8 @@ process {
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// collapsing options
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params.shortread_qc_mergepairs ? "--collapse" : "",
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// trimming options
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params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
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params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
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params.shortread_qc_adapter2 ? "--adapter2 ${params.shortread_qc_adapter2}" : "",
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params.shortread_qc_skipadaptertrim ? "--adapter1 ''" : params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "", // adding adapter list happens at module input channel level
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params.shortread_qc_skipadaptertrim ? "--adapter2 ''" : params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter2 ? "--adapter2 ${params.shortread_qc_adapter2}" : "",
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// filtering options
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"--minlength ${params.shortread_qc_minlength}"
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].join(' ').trim()
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@ -7,7 +7,7 @@
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"nf-core": {
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"adapterremoval": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "ce7cf27e377fdacf7ebe8e75903ec70405ea1659"
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},
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"bbmap/bbduk": {
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"branch": "master",
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4
modules/nf-core/adapterremoval/main.nf
generated
4
modules/nf-core/adapterremoval/main.nf
generated
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@ -34,7 +34,7 @@ process ADAPTERREMOVAL {
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AdapterRemoval \\
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--file1 $reads \\
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$args \\
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$adapterlist \\
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$list \\
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--basename ${prefix} \\
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--threads ${task.cpus} \\
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--seed 42 \\
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@ -61,7 +61,7 @@ process ADAPTERREMOVAL {
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--file1 ${reads[0]} \\
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--file2 ${reads[1]} \\
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$args \\
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$adapterlist \\
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$list \\
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--basename ${prefix} \\
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--threads $task.cpus \\
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--seed 42 \\
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@ -59,9 +59,9 @@ params {
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// Databases
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databases = null
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// FASTQ preprocessing
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preprocessing_qc_tool = 'fastqc'
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// FASTQ preprocessing
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perform_shortread_qc = false
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shortread_qc_tool = 'fastp'
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shortread_qc_skipadaptertrim = false
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@ -69,6 +69,7 @@ params {
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shortread_qc_excludeunmerged = false
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shortread_qc_adapter1 = null
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shortread_qc_adapter2 = null
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shortread_qc_adapterlist = null // TODO Add for FASTP
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shortread_qc_minlength = 15
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perform_longread_qc = 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", "outdir", "databases"],
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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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@ -80,7 +84,10 @@
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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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@ -104,6 +111,12 @@
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"description": "Specify adapter 2 nucleotide sequence",
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"help_text": "Specify a custom reverse or R2 adapter sequence to be removed from reads. \n\nIf not set, the selected short-read QC tool's defaults will be used.\n\n> Modifies tool parameter(s):\n> - fastp: `--adapter_sequence`. fastp default: `AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT`\n> - AdapterRemoval: `--adapter1`. AdapteRemoval2 default: `AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT`"
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},
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"shortread_qc_adapterlist": {
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"type": "string",
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"default": "None",
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"fa_icon": "fas fa-list-ul",
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"help_text": "This affects AdapterRemoval. It will replace default adapters or whatever is supplied in `--shortread_qc_adapter{1,2}`.\n\nThis allows you to mix libraries built with different adapters into one run.\n\n> Modifies tool parameter(s):\n> - AdapterRemoval: `--adapter-list`."
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},
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"shortread_qc_mergepairs": {
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"type": "boolean",
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"fa_icon": "fas fa-toggle-on",
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@ -133,7 +146,11 @@
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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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@ -167,7 +184,10 @@
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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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@ -341,7 +361,15 @@
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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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@ -360,7 +388,14 @@
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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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@ -555,7 +590,14 @@
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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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@ -711,10 +753,7 @@
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"properties": {
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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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"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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"default": "fastqc"
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}
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}
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}
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@ -10,6 +10,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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take:
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reads // [[meta], [reads]]
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adapterlist // file
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main:
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ch_versions = Channel.empty()
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@ -21,8 +22,8 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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paired: !it[0].single_end
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}
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ADAPTERREMOVAL_SINGLE ( ch_input_for_adapterremoval.single, [] )
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ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, [] )
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ADAPTERREMOVAL_SINGLE ( ch_input_for_adapterremoval.single, adapterlist )
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ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, adapterlist )
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/*
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* Due to the ~slightly~ very ugly output implementation of the current AdapterRemoval2 version, each file
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@ -11,6 +11,7 @@ include { FALCO as FALCO_PROCESSED } from '../../modules/nf-core/falco/main'
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workflow SHORTREAD_PREPROCESSING {
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take:
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reads // [ [ meta ], [ reads ] ]
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adapterlist // file
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main:
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ch_versions = Channel.empty()
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@ -12,7 +12,8 @@ WorkflowTaxprofiler.initialise(params, log)
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// TODO nf-core: Add all file path parameters for the pipeline to the list below
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// Check input path parameters to see if they exist
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def checkPathParamList = [ params.input, params.databases, params.hostremoval_reference,
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params.shortread_hostremoval_index, params.multiqc_config
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params.shortread_hostremoval_index, params.multiqc_config,
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params.shortread_qc_adapterlist
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]
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for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
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@ -102,6 +103,7 @@ workflow TAXPROFILER {
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ch_versions = Channel.empty()
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ch_multiqc_logo= Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
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ch_adapterlist_for_shortreadqc = params.shortread_qc_adapterlist ? file(params.shortread_qc_adapterlist) : []
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/*
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SUBWORKFLOW: Read in samplesheet, validate and stage input files
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@ -131,8 +133,11 @@ workflow TAXPROFILER {
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/*
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SUBWORKFLOW: PERFORM PREPROCESSING
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*/
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ch_adapterlist_for_shortreadqc
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if ( params.perform_shortread_qc ) {
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ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
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ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq, ch_adapterlist_for_shortreadqc ).reads
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ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
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} else {
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ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
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