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Add samplesheet validation #135

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merged 4 commits into from
Nov 6, 2022
Merged

Add samplesheet validation #135

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01d9d2a
accommodate the samplesheet validation process
abhi18av Nov 6, 2022
9aed630
remove the mock param
abhi18av Nov 6, 2022
1f56b81
update the conda env
abhi18av Nov 6, 2022
10e1aea
tweak output message
abhi18av Nov 6, 2022
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3 changes: 2 additions & 1 deletion bin/samplesheet_validation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,8 @@
fail = True

if not fail:
print('No errors found')
print('Samplesheet validation checks passed')
exit(0)
else:
print('Samplesheet validation checks failed')
exit(1)
2 changes: 1 addition & 1 deletion conf/conda_local.config
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Expand Up @@ -9,7 +9,7 @@ conda {
process {

withName:
'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*' {
'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*|SAMPLESHEET.*' {
//environment does exist:
conda = "${params.conda_envs_location}/xbs-nf-env-1"

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2 changes: 1 addition & 1 deletion conf/docker.config
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Expand Up @@ -5,7 +5,7 @@ process {
//----------------------------------------------

withName:
'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*' {
'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*|SAMPLESHEET.*' {
container = "rg.nl-ams.scw.cloud/xbs-nf-containers/xbs-nf-container-1:0.9.8"
}

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49 changes: 2 additions & 47 deletions main.nf
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Expand Up @@ -13,50 +13,6 @@ include { MERGE_WF } from './workflows/merge_wf.nf'
include { QUALITY_CHECK_WF } from './workflows/quality_check_wf.nf'
include { REPORTS_WF } from './workflows/reports_wf.nf'

//================================================================================
// Prepare channels
//================================================================================


//NOTE: Expected structure of input CSV samplesheet
// 0 1 2 3 4 5 6 7 8
// Study,Sample,Library,Attempt,R1,R2,Flowcell,Lane,Index Sequence

reads_ch = Channel.fromPath(params.input_samplesheet)
.splitCsv(header: false, skip: 1)
.map { row -> {
study = row[0]
sample = row[1]
library = row[2]
attempt = row[3]
read1 = row[4]
read2 = row[5]
flowcell = row[6]
lane = row[7]
index_sequence = row[8]

//NOTE: Platform is hard-coded to illumina
bam_rg_string ="@RG\\tID:${flowcell}.${lane}\\tSM:${study}.${sample}\\tPL:illumina\\tLB:lib${library}\\tPU:${flowcell}.${lane}.${index_sequence}"

unique_sample_id = "${study}.${sample}.L${library}.A${attempt}.${flowcell}.${lane}.${index_sequence}"

//Accomodate single/multi reads
if (read1 && read2) {

return tuple(unique_sample_id, bam_rg_string, tuple(file(read1), file(read2)))

} else if (read1) {

return tuple(unique_sample_id, bam_rg_string, tuple(file(read1)))

} else {

return tuple(unique_sample_id, bam_rg_string, tuple(file(read2)))

}
}
}


//================================================================================
// Main workflow
Expand All @@ -66,11 +22,11 @@ workflow {

if (params.only_validate_fastqs) {

VALIDATE_FASTQS_WF(reads_ch)
VALIDATE_FASTQS_WF(params.input_samplesheet)

} else {

validated_reads_ch = VALIDATE_FASTQS_WF(reads_ch)
validated_reads_ch = VALIDATE_FASTQS_WF(params.input_samplesheet)

QUALITY_CHECK_WF(validated_reads_ch)

Expand All @@ -79,7 +35,6 @@ workflow {

MULTIPLE_INFECTIONS_WF(MAP_WF.out.rejected_sorted_reads_ch)


CALL_WF(MAP_WF.out.approved_sorted_reads_ch)

collated_gvcfs_ch = CALL_WF.out.gvcf_ch
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14 changes: 14 additions & 0 deletions modules/utils/samplesheet_validation.nf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
process SAMPLESHEET_VALIDATION {

input:
path(samplesheet)

output:
path(samplesheet)

script:

"""
samplesheet_validation.py ${samplesheet}
"""
}
44 changes: 42 additions & 2 deletions workflows/validate_fastqs_wf.nf
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Original file line number Diff line number Diff line change
@@ -1,13 +1,53 @@
include { FASTQ_VALIDATOR } from '../modules/fastq_utils/validator.nf' addParams ( params.FASTQ_VALIDATOR )
include { UTILS_FASTQ_COHORT_VALIDATION } from '../modules/utils/fastq_cohort_validation.nf' addParams ( params.UTILS_FASTQ_COHORT_VALIDATION )
include { SAMPLESHEET_VALIDATION } from '../modules/utils/samplesheet_validation.nf'

workflow VALIDATE_FASTQS_WF {
take:
reads_ch
samplesheet

main:
SAMPLESHEET_VALIDATION(samplesheet)

//NOTE: Expected structure of input CSV samplesheet
// 0 1 2 3 4 5 6 7 8
// Study,Sample,Library,Attempt,R1,R2,Flowcell,Lane,Index Sequence

reads_ch = SAMPLESHEET_VALIDATION.out
.splitCsv(header: false, skip: 1)
.map { row -> {
study = row[0]
sample = row[1]
library = row[2]
attempt = row[3]
read1 = row[4]
read2 = row[5]
flowcell = row[6]
lane = row[7]
index_sequence = row[8]

//NOTE: Platform is hard-coded to illumina
bam_rg_string ="@RG\\tID:${flowcell}.${lane}\\tSM:${study}.${sample}\\tPL:illumina\\tLB:lib${library}\\tPU:${flowcell}.${lane}.${index_sequence}"

unique_sample_id = "${study}.${sample}.L${library}.A${attempt}.${flowcell}.${lane}.${index_sequence}"

//Accomodate single/multi reads
if (read1 && read2) {

return tuple(unique_sample_id, bam_rg_string, tuple(file(read1), file(read2)))

} else if (read1) {

return tuple(unique_sample_id, bam_rg_string, tuple(file(read1)))

} else {

return tuple(unique_sample_id, bam_rg_string, tuple(file(read2)))

}
}
}

//FIXME: Add the samplesheet validator process for samplesheet_validation.py script

FASTQ_VALIDATOR(reads_ch)

Expand Down