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Merge branch 'dev' into nf-core-template-merge-2.14.0
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MatthiasZepper committed May 8, 2024
2 parents 93c66a4 + d169eef commit 69845bd
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Showing 5 changed files with 47 additions and 19 deletions.
6 changes: 3 additions & 3 deletions assets/samplesheet.csv
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
sample,fastq_1,fastq_2
SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
sample,lane,project,fastq_1,fastq_2,rundir
SAMPLE_PAIRED_END,1,P001,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz,/path/to/rundir
SAMPLE_SINGLE_END,2,P002,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,,/path/to/rundir
26 changes: 24 additions & 2 deletions assets/schema_input.json
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,19 @@
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces",
"meta": ["id"]
"meta": ["sample"]
},
"lane": {
"type": "integer",
"pattern": "^\\d+$",
"errorMessage": "Lane ID must be a number",
"meta": ["lane"]
},
"project": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Project ID cannot contain spaces",
"meta": ["project"]
},
"fastq_1": {
"type": "string",
Expand All @@ -26,8 +38,18 @@
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
},
"rundir": {
"type": "string",
"format": "path",
"exists": true,
"errorMessage": "Run directory must be a path",
"meta": ["rundir"]
}
},
"required": ["sample", "fastq_1"]
"required": ["sample", "lane", "fastq_1"],
"dependentRequired": {
"fastq_2": ["fastq_1"]
}
}
}
2 changes: 1 addition & 1 deletion conf/test.config
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ params {
// Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
input = params.pipelines_testdata_base_path + 'seqinspector/testdata/MiSeq/samplesheet.csv'

// Genome references
genome = 'R64-1-1'
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4 changes: 2 additions & 2 deletions main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ nextflow.enable.dsl = 2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { SEQINSPECTOR } from './workflows/seqinspector'
include { SEQINSPECTOR } from './workflows/seqinspector'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'

Expand All @@ -32,7 +32,7 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_seqi
// TODO nf-core: Remove this line if you don't need a FASTA file
// This is an example of how to use getGenomeAttribute() to fetch parameters
// from igenomes.config using `--genome`
params.fasta = getGenomeAttribute('fasta')
// params.fasta = getGenomeAttribute('fasta')

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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28 changes: 17 additions & 11 deletions subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ workflow PIPELINE_INITIALISATION {
pre_help_text = nfCoreLogo(monochrome_logs)
post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
UTILS_NFVALIDATION_PLUGIN (
UTILS_NFVALIDATION_PLUGIN ( // Validates parameters against $projectDir/nextflow_schema.json
help,
workflow_command,
pre_help_text,
Expand All @@ -75,29 +75,33 @@ workflow PIPELINE_INITIALISATION {
//
// Custom validation for pipeline parameters
//
validateInputParameters()
validateInputParameters() // Runs additional validation that is not done by $projectDir/nextflow_schema.json

//
// Create channel from input file provided through params.input
//
Channel
.fromSamplesheet("input")
.fromSamplesheet("input") // Validates samplesheet against $projectDir/assets/schema_input.json. Path to validation schema is defined by $projectDir/nextflow_schema.json
.map {
meta, fastq_1, fastq_2 ->
def id_string = "${meta.sample}_${meta.project ?: "ungrouped"}_${meta.lane}"
def updated_meta = meta + [ id: id_string ]
if (!fastq_2) {
return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
return [ updated_meta.id, updated_meta + [ single_end:true ], [ fastq_1 ] ]
} else {
return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
return [ updated_meta.id, updated_meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
}
}
.groupTuple()
.map {
validateInputSamplesheet(it)
}
.map {
meta, fastqs ->
return [ meta, fastqs.flatten() ]
validateInputSamplesheet(it) // Applies additional group validation checks that schema_input.json cannot do.
}
.transpose() // Replace the map below
// .map {
// meta, fastqs ->
// return [ meta, fastqs.flatten() ]
// }
.view()
.set { ch_samplesheet }

emit:
Expand Down Expand Up @@ -155,7 +159,9 @@ workflow PIPELINE_COMPLETION {
// Check and validate pipeline parameters
//
def validateInputParameters() {
genomeExistsError()
// genomeExistsError()

// TODO: Add code to further validate pipeline parameters here
}

//
Expand Down

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