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Deploy nf-validation plugin #63

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Aug 4, 2023
Merged

Deploy nf-validation plugin #63

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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Changed`

- [#63](https://github.com/nf-core/bamtofastq/pull/63) Replace extract_csv with nf-validation plugin

### `Fixed`

- [#62](https://github.com/nf-core/bamtofastq/pull/62) Adjust subway map for dark mode.
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/bamtofastq" target="_blank">nf-core/bamtofastq</a>
This report has been generated by the <a href="https://github.com/nf-core/bamtofastq/tree/dev" target="_blank">nf-core/bamtofastq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/bamtofastq/2.0.0/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/bamtofastq/dev/docs/output" target="_blank">documentation</a>.
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Is this supposed to be there?

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Yes, this will be passing the linting from the tools version 2.10 onwards :) The old links are not working and are already fixed in the dev version :)

report_section_order:
"nf-core-bamtofastq-methods-description":
order: -1000
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39 changes: 21 additions & 18 deletions assets/schema_input.json
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Expand Up @@ -7,30 +7,33 @@
"items": {
"type": "object",
"properties": {
"sample": {
"sample_id": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces"
"errorMessage": "The sample sheet should specify a sample_id for each row which cannot contain spaces.",
"meta": ["id"]
},
"fastq_1": {
"mapped": {
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.(bam|cram)$",
"errorMessage": "The sample sheet should specify a mapped file for each row, either '.bam' or '.cram'"
},
"fastq_2": {
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
{
"type": "string",
"maxLength": 0
}
]
"index": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.(bai|crai)$",
"errorMessage": "Index files can be provided but must have the extension '.bai' or '.crai'"
},
"file_type": {
"type": "string",
"errorMessage": "Input filetypes must either be 'bam' or 'cram'",
"meta": ["filetype"],
"enums": ["bam", "cram"]
}
},
"required": ["sample", "fastq_1"]
"required": ["sample_id", "mapped", "file_type"]
}
}
3 changes: 2 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -20,7 +20,8 @@
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/bamtofastq/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
"fa_icon": "fas fa-file-csv",
"schema": "assets/schema_input.json"
},
"outdir": {
"type": "string",
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58 changes: 12 additions & 46 deletions workflows/bamtofastq.nf
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Expand Up @@ -4,7 +4,7 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation'

def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
Expand All @@ -16,8 +16,18 @@ log.info logo + paramsSummaryLog(workflow) + citation
WorkflowBamtofastq.initialise(params, log)

// Check mandatory parameters
ch_input = extract_csv(file(params.input))
ch_input = Channel.fromSamplesheet("input")
.map{ meta, mapped, index ->

if (meta.filetype != mapped.getExtension().toString()) {
error('The file extension does not fit the specified file_type.\n' + mapped.toString() )
}

meta.index = index ? true : false

return [meta, mapped, index]

}

// Initialize file channels based on params
fasta = params.fasta ? Channel.fromPath(params.fasta).collect() : Channel.value([])
Expand Down Expand Up @@ -255,50 +265,6 @@ workflow.onComplete {
FUNCTIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// Function to extract information (meta data + file(s)) from csv file(s)
def extract_csv(csv_file) {

// check that the sample sheet is not 1 line or less, because it'll skip all subsequent checks if so.
file(csv_file).withReader('UTF-8') { reader ->
def line, numberOfLinesInSampleSheet = 0;
while ((line = reader.readLine()) != null) {numberOfLinesInSampleSheet++}
if (numberOfLinesInSampleSheet < 2) {
error("Samplesheet had less than two lines. The sample sheet must be a csv file with a header, so at least two lines.")
}
}
Channel.from(csv_file).splitCsv(header: true)
.map{ row ->
if ( !row.sample_id ) { // This also handles the case where the lane is left as an empty string
error('The sample sheet should specify a sample_id for each row.\n' + row.toString())
}
if ( !row.mapped ) { // This also handles the case where the lane is left as an empty string
error('The sample sheet should specify a mapped file for each row.\n' + row.toString())
}
if (!row.file_type) { // This also handles the case where the lane is left as an empty string
error('The sample sheet should specify a file_type for each row, valid values are bam/cram.\n' + row.toString())
}
if (!(row.file_type == "bam" || row.file_type == "cram")) {
error('The file_type for the row below is neither "bam" nor "cram". Please correct this.\n' + row.toString() )
}
if (row.file_type != file(row.mapped).getExtension().toString()) {
error('The file extension does not fit the specified file_type.\n' + row.toString() )
}


// init meta map
def meta = [:]

meta.id = "${row.sample_id}".toString()
def mapped = file(row.mapped, checkIfExists: true)
def index = row.index ? file(row.index, checkIfExists: true) : []
meta.filetype = "${row.file_type}".toString()
meta.index = row.index ? true : false

return [meta, mapped, index]

}

}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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