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5. Exercise 3

Move into the exercise 3 directory and execute the hello-gatk.nf script.

cd /workspace/gitpod/troubleshoot/exercise3
nextflow run hello-gatk.nf

Error message

WARN: Input tuple does not match tuple declaration in process `GATK_HAPLOTYPECALLER` -- offending value: [NA12878, /workspace/gitpod/troubleshoot/exercise3/work/aa/e0741cf287ce3a0c23f4dc12604b8c/reads_mother.bam, /workspace/gitpod/troubleshoot/exercise3/work/aa/e0741cf287ce3a0c23f4dc12604b8c/reads_mother.bam.bai]
ERROR ~ Error executing process > 'GATK_HAPLOTYPECALLER (1)'

Caused by:
Not a valid path value: 'NA12878'


Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

-- Check '.nextflow.log' file for details
Solution

This warning can be broken down to help identify the cause:

You can immediately see that the GATK_HAPLOTYPECALLER has an offending value [NA12878, /workspace/gitpod/troubleshoot/exercise3/work/aa/e0741cf287ce3a0c23f4dc12604b8c/reads_mother.bam, /workspace/gitpod/troubleshoot/exercise3/work/aa/e0741cf287ce3a0c23f4dc12604b8c/reads_mother.bam.bai].

Your offending value may be NA12878, NA12877, or NA12882

In this example, the value 'NA12878' is not a valid path.

There is only one tuple for the GATK_HAPLOTYPECALLER process:

hello.gatk.nf
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tuple path(input_bam), path(input_bam_index)

It can be seen that this tuple is made up of two paths and offending value has one value and two paths.

It can be concluded that the tuple has a missing value in the first position.

To resolve this error a val must be added to this input.

The name of this val might be used in the script block and must be considered.

While all of the variables in the script block are accounted for, the id value in the output has not been specified.

It can be concluded that the input val should be val(id) to match the output.

hello-gatk.nf
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/*
* Call variants with GATK HapolotypeCaller in GVCF mode
*/
process GATK_HAPLOTYPECALLER {

    container "broadinstitute/gatk:4.5.0.0"

    input:
        tuple val(id), path(input_bam), path(input_bam_index)
        path ref_fasta
        path ref_index
        path ref_dict
        path interval_list

    output:
        tuple val(id), path("${input_bam}.g.vcf"), path("${input_bam}.g.vcf.idx")

    """
    gatk HaplotypeCaller \
        -R ${ref_fasta} \
        -I ${input_bam} \
        -O ${input_bam}.g.vcf \
        -L ${interval_list} \
        -ERC GVCF
    """
}