gencorefacility / variant-calling-pipeline-gatk4

Variant Calling Pipeline Using GATK4 and Nextflow

variant-calling-pipeline-gatk4

Variant Calling Pipeline Using GATK4 and Nextflow

This repo contains a Nextflow script for variant detection using GATK4. Full details including a description of the analysis and how to use the script: https://gencore.bio.nyu.edu/variant-calling-pipeline-gatk4/

Overview of the workflow:

variant-calling-pipeline-gatk4's Issues

Error while running the nextflow framework at getMetrics step

Hello!
I'm using the nextflow framework for variant calling in E.coli, I am pretty new to this. I have configured my nextflow.config file.The process crashes in the getMetrics step. The error shows PICARD_JAR: unbound variable but I did export pICARD_JAR to my ./bashrc.
The error is as follows:

Error executing process > 'getMetrics (1)'

Caused by:
Process getMetrics (1) terminated with an error exit status (1)

Command executed:

java -jar $PICARD_JAR CollectAlignmentSummaryMetrics 7R=/STORAGE/e_coli/GCF_000005845.2_ASM584v2_genomic.fna I=MT-2021-00037_S4_L001_R_sorted_dedup.bam 0003O=MT-2021-00037_S4_L001_R_alignment_metrics.txt
java -jar $PICARD_JAR CollectInsertSizeMetrics INPUT=MT-2021-00037_S4_L001_R_sorted_dedup.bam OUTPUT=MT-2021-00037_S4_L001_R_insert_metrics.txt HISTOGRAM_FILE=MT-2021-00037_S4_L001_R_insert_size_histogram.pdf
samtools depth -a MT-2021-00037_S4_L001_R_sorted_dedup.bam > MT-2021-00037_S4_L001_R_depth_out.txt

Command exit status:
1

Command output:
(empty)

Command error:
.command.sh: line 2: PICARD_JAR: unbound variable

Work dir:
/STORAGE/e_coli/control_result/nextflow_work_dir/29/d10f0357a7b623c360e06d31fdd913

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh