script bugfix

nf-cmgg · Mar 12, 2024 · 8f8ae34 · 8f8ae34
1 parent 492bed4
commit 8f8ae34
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Showing 6 changed files with 6 additions and 2 deletions.
diff --git a/utils/nf-cmgg-sampletracking/nf-cmgg-sampletracking.go b/utils/nf-cmgg-sampletracking/nf-cmgg-sampletracking.go
@@ -3,6 +3,7 @@ package main
 import (
 	"context"
 	"encoding/csv"
+	"fmt"
 	"io"
 	"io/fs"
 	"os"
@@ -174,11 +175,12 @@ func main() {
 				// Find the snp fastq
 				for _, file := range snpFastq {
 					if strings.Contains(file, sample.sample) {
-						if strings.Contains(file, "_1") {
+						if strings.Contains(file, "_R1") {
 							samples[i].snpFastq1 = file
-						} else if strings.Contains(file, "_2") {
+						} else if strings.Contains(file, "_R2") {
 							samples[i].snpFastq2 = file
 						}
+						fmt.Println(sample)
 					}
 				}
 				// Find the snp bam

diff --git a/utils/nf-cmgg-sampletracking/sampletracking_samplesheet.csv b/utils/nf-cmgg-sampletracking/sampletracking_samplesheet.csv
@@ -0,0 +1,2 @@
+sample,pool,sample_bam,sample_bam_index,snp_fastq_1,snp_fastq_2,snp_bam,snp_bam_index
+D2217639,WES_H112,test-data/sample_data/D2217639.cram,test-data/sample_data/D2217639.cram.crai,test-data/snp_data/snp_D2217639_S201_R1_001.fastq.gz,test-data/snp_data/snp_D2217639_S201_R2_001.fastq.gz,,
diff --git a/utils/nf-cmgg-sampletracking/test-data/sample_data/D2217639.cram b/utils/nf-cmgg-sampletracking/test-data/sample_data/D2217639.cram
diff --git a/utils/nf-cmgg-sampletracking/test-data/sample_data/D2217639.cram.crai b/utils/nf-cmgg-sampletracking/test-data/sample_data/D2217639.cram.crai
diff --git a/utils/nf-cmgg-sampletracking/test-data/snp_data/snp_D2217639_S201_R1_001.fastq.gz b/utils/nf-cmgg-sampletracking/test-data/snp_data/snp_D2217639_S201_R1_001.fastq.gz
diff --git a/utils/nf-cmgg-sampletracking/test-data/snp_data/snp_D2217639_S201_R2_001.fastq.gz b/utils/nf-cmgg-sampletracking/test-data/snp_data/snp_D2217639_S201_R2_001.fastq.gz
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample,pool,sample_bam,sample_bam_index,snp_fastq_1,snp_fastq_2,snp_bam,snp_bam_index
		D2217639,WES_H112,test-data/sample_data/D2217639.cram,test-data/sample_data/D2217639.cram.crai,test-data/snp_data/snp_D2217639_S201_R1_001.fastq.gz,test-data/snp_data/snp_D2217639_S201_R2_001.fastq.gz,,