Updated FastQC paths

hbctraining · May 13, 2024 · b8cb967 · b8cb967
1 parent a8ba611
commit b8cb967
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/lessons/05_alignment_QC.md b/lessons/05_alignment_QC.md
@@ -263,10 +263,10 @@ TUMOR_SAMPLE_NAME=syn3_tumor
 REFERENCE=GRCh38.p7
 NORMAL_PICARD_METRICS=${REPORTS_DIRECTORY}picard/${NORMAL_SAMPLE_NAME}/${NORMAL_SAMPLE_NAME}_${REFERENCE}.CollectAlignmentSummaryMetrics.txt
 TUMOR_PICARD_METRICS=${REPORTS_DIRECTORY}picard/${TUMOR_SAMPLE_NAME}/${TUMOR_SAMPLE_NAME}_${REFERENCE}.CollectAlignmentSummaryMetrics.txt
-NORMAL_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}/${NORMAL_SAMPLE_NAME}_1_fastqc.zip
-NORMAL_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}/${NORMAL_SAMPLE_NAME}_2_fastqc.zip
-TUMOR_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}/${TUMOR_SAMPLE_NAME}_1_fastqc.zip
-TUMOR_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}/${TUMOR_SAMPLE_NAME}_2_fastqc.zip
+NORMAL_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}_1_fastqc.zip
+NORMAL_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}_2_fastqc.zip
+TUMOR_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}_1_fastqc.zip
+TUMOR_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}_2_fastqc.zip
 OUTPUT_DIRECTORY=${REPORTS_DIRECTORY}/multiqc/
 ```
 
@@ -313,10 +313,10 @@ TUMOR_SAMPLE_NAME=syn3_tumor
 REFERENCE=GRCh38.p7
 NORMAL_PICARD_METRICS=${REPORTS_DIRECTORY}picard/${NORMAL_SAMPLE_NAME}/${NORMAL_SAMPLE_NAME}_${REFERENCE}.CollectAlignmentSummaryMetrics.txt
 TUMOR_PICARD_METRICS=${REPORTS_DIRECTORY}picard/${TUMOR_SAMPLE_NAME}/${TUMOR_SAMPLE_NAME}_${REFERENCE}.CollectAlignmentSummaryMetrics.txt
-NORMAL_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}/${NORMAL_SAMPLE_NAME}_1_fastqc.zip
-NORMAL_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}/${NORMAL_SAMPLE_NAME}_2_fastqc.zip
-TUMOR_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}/${TUMOR_SAMPLE_NAME}_1_fastqc.zip
-TUMOR_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}/${TUMOR_SAMPLE_NAME}_2_fastqc.zip
+NORMAL_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}_1_fastqc.zip
+NORMAL_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${NORMAL_SAMPLE_NAME}_2_fastqc.zip
+TUMOR_FASTQC_1=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}_1_fastqc.zip
+TUMOR_FASTQC_2=${REPORTS_DIRECTORY}fastqc/${TUMOR_SAMPLE_NAME}_2_fastqc.zip
 OUTPUT_DIRECTORY=${REPORTS_DIRECTORY}/multiqc/<br>
 # Create directory for output
 mkdir -p $OUTPUT_DIRECTORY<br>