diff --git a/bin/samplesheet_validation.py b/bin/samplesheet_validation.py
index b8360304..115bd1b9 100755
--- a/bin/samplesheet_validation.py
+++ b/bin/samplesheet_validation.py
@@ -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)
diff --git a/conf/conda_local.config b/conf/conda_local.config
index fb8dacfd..4ae87445 100644
--- a/conf/conda_local.config
+++ b/conf/conda_local.config
@@ -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 = "${params.conda_envs_location}/xbs-nf-env-1"
diff --git a/conf/docker.config b/conf/docker.config
index f9d8650f..0f6f3bd3 100644
--- a/conf/docker.config
+++ b/conf/docker.config
@@ -5,7 +5,7 @@ process {
//----------------------------------------------
withName:
- 'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*' {
+ 'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*|SAMPLESHEET.*' {
container = "rg.nl-ams.scw.cloud/xbs-nf-containers/xbs-nf-container-1:0.9.8"
}
diff --git a/main.nf b/main.nf
index 941443ec..f0dd35f2 100644
--- a/main.nf
+++ b/main.nf
@@ -13,50 +13,6 @@ include { MERGE_WF } from './workflows/merge_wf.nf'
include { QUALITY_CHECK_WF } from './workflows/quality_check_wf.nf'
include { REPORTS_WF } from './workflows/reports_wf.nf'
-//================================================================================
-// Prepare channels
-//================================================================================
-
-
-//NOTE: Expected structure of input CSV samplesheet
-// 0 1 2 3 4 5 6 7 8
-// Study,Sample,Library,Attempt,R1,R2,Flowcell,Lane,Index Sequence
-
-reads_ch = Channel.fromPath(params.input_samplesheet)
- .splitCsv(header: false, skip: 1)
- .map { row -> {
- study = row[0]
- sample = row[1]
- library = row[2]
- attempt = row[3]
- read1 = row[4]
- read2 = row[5]
- flowcell = row[6]
- lane = row[7]
- index_sequence = row[8]
-
- //NOTE: Platform is hard-coded to illumina
- bam_rg_string ="@RG\\tID:${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
@@ -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)
@@ -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
diff --git a/modules/utils/samplesheet_validation.nf b/modules/utils/samplesheet_validation.nf
new file mode 100644
index 00000000..c71c47ee
--- /dev/null
+++ b/modules/utils/samplesheet_validation.nf
@@ -0,0 +1,14 @@
+process SAMPLESHEET_VALIDATION {
+
+ input:
+ path(samplesheet)
+
+ output:
+ path(samplesheet)
+
+ script:
+
+ """
+ samplesheet_validation.py ${samplesheet}
+ """
+}
diff --git a/workflows/validate_fastqs_wf.nf b/workflows/validate_fastqs_wf.nf
index 1bc8b86f..c9e0676f 100644
--- a/workflows/validate_fastqs_wf.nf
+++ b/workflows/validate_fastqs_wf.nf
@@ -1,13 +1,53 @@
include { FASTQ_VALIDATOR } from '../modules/fastq_utils/validator.nf' addParams ( params.FASTQ_VALIDATOR )
include { UTILS_FASTQ_COHORT_VALIDATION } from '../modules/utils/fastq_cohort_validation.nf' addParams ( params.UTILS_FASTQ_COHORT_VALIDATION )
+include { SAMPLESHEET_VALIDATION } from '../modules/utils/samplesheet_validation.nf'
workflow VALIDATE_FASTQS_WF {
take:
- reads_ch
+ samplesheet
main:
+ SAMPLESHEET_VALIDATION(samplesheet)
+
+ //NOTE: Expected structure of input CSV samplesheet
+ // 0 1 2 3 4 5 6 7 8
+ // Study,Sample,Library,Attempt,R1,R2,Flowcell,Lane,Index Sequence
+
+ reads_ch = SAMPLESHEET_VALIDATION.out
+ .splitCsv(header: false, skip: 1)
+ .map { row -> {
+ study = row[0]
+ sample = row[1]
+ library = row[2]
+ attempt = row[3]
+ read1 = row[4]
+ read2 = row[5]
+ flowcell = row[6]
+ lane = row[7]
+ index_sequence = row[8]
+
+ //NOTE: Platform is hard-coded to illumina
+ bam_rg_string ="@RG\\tID:${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)