REQUIRED for all errors and issues:
a) GATK version used: gatk4="4.1.4.1"

b) Exact command used:

In a homemade Nextflow pipeline, i use the process:

process GatherVcfs , and i modify the line 248 from this script (https://github.com/IARCbioinfo/gatk4-GenotypeGVCFs-nf/blob/master/gatk4-GenotypeGVCFs.nf#L248) to fit to my study. The chromosomes names are from a FalconUnzip Genome : Primary_000001F, longueur than usually and with a letter F at the end.

I tried to shorter it with substring(13:15) instead of substring(5) but it doesn't work.

    script:

    """

    gatk --java-options "-Xmx${params.mem}g -Xms${params.mem}g" \

      GatherVcfs \

      ${vcf.findAll{ it=~/Primary_000\d+/ }.collect().sort{ it.name.tokenize('.')[1].substring(13:15).toInteger()

 }.collect{ "--INPUT $it " }.join() } \

      --OUTPUT ${params.cohort}.vcf -resume

    """

}

 
c) Entire program log:

N E X T F L O W  ~  version 19.07.0

Launching `test_gather.nf` [crazy_ardinghelli] - revision: f422934a6c

[-        ] process > index            -

[-        ] process > GenomicsDBImport -

[-        ] process > GenotypeGVCFs    -

[-        ] process > GatherVcfs       -

executor >  slurm (384)

[skipped  ] process > index                  [100%] 1 of 1, stored: 1 ✔

[d4/7882ac] process > GenomicsDBImport (192) [100%] 192 of 192 ✔

[11/01b9c6] process > GenotypeGVCFs (188)    [100%] 192 of 192 ✔

[-        ] process > GatherVcfs             -

Error executing process > 'GatherVcfs'

Caused by:

  No signature of method: java.lang.String.substring() is applicable for argument types: (LinkedHashMap) values: 

[[13:15]]

Possible solutions: substring(int), substring(int, int), toString(), toString(), toString()

Source block:

  """

  gatk --java-options "-Xmx${params.mem}g -Xms${params.mem}g" \

    GatherVcfs \

    ${vcf.findAll{ it=~/Primary_000\d+/ }.collect().sort{ it.name.tokenize('.')[1].substring(13:15).toInteger() }

.collect{ "--INPUT $it " }.join() } \

    --OUTPUT ${params.cohort}.vcf -resume

  """

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

out`

[PoolSeq-Map] FAILED: crazy_ardinghelli

---------------------------

Pipeline execution summary

---------------------------

Completed at: Thu Dec 08 15:29:45 CET 2022

Duration    : 22m 26s

Success     : false

workDir     : /scratch/mildiou/VCF_all_mildew/fromGvcfToVCF/work

exit status : null

executor >  slurm (384)

[skipped  ] process > index                  [100%] 1 of 1, stored: 1 ✔

[d4/7882ac] process > GenomicsDBImport (192) [100%] 192 of 192 ✔

[11/01b9c6] process > GenotypeGVCFs (188)    [100%] 192 of 192 ✔

[-        ] process > GatherVcfs             -

Error executing process > 'GatherVcfs'

Caused by:

  No signature of method: java.lang.String.substring() is applicable for argument types: (LinkedHashMap) values: 

[[13:15]]

Possible solutions: substring(int), substring(int, int), toString(), toString(), toString()

Source block:

  """

  gatk --java-options "-Xmx${params.mem}g -Xms${params.mem}g" \

    GatherVcfs \

    ${vcf.findAll{ it=~/Primary_000\d+/ }.collect().sort{ it.name.tokenize('.')[1].substring(13:15).toInteger() }

.collect{ "--INPUT $it " }.join() } \

    --OUTPUT ${params.cohort}.vcf -resume

  """