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include intervals_index (#1308)

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* include intervals_index

In order to run the GATK `GenotypeGVCFs` tool with an interval file (such as a .bed file) you need to have the corresponding index file. Otherwise you get the following error message
```
A USER ERROR has occurred: An index is required but was not found for file genome.bed.gz: work/6c/541fce2dc670597f62a571c72288c6/genome.bed.gz. Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.
```

including the index file fixes this problem

* Update meta.yml
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nickhsmith 2022-02-16 18:35:09 +01:00 committed by GitHub
parent a69faefee8
commit 8717792135
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2 changed files with 5 additions and 2 deletions
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2
modules/gatk4/genotypegvcfs/main.nf
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@ -8,7 +8,7 @@ process GATK4_GENOTYPEGVCFS {
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
input: input:
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals) tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
path fasta path fasta
path fasta_index path fasta_index
path fasta_dict path fasta_dict

5
modules/gatk4/genotypegvcfs/meta.yml
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@ -27,7 +27,10 @@ input:
pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"] pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"]
- intervals: - intervals:
type: file type: file
description: Bed file with the genomic regions included in the library (optional) description: Interval file with the genomic regions included in the library (optional)
- intervals_index:
type: file
description: Interval index file (optional)
- fasta: - fasta:
type: file type: file
description: Reference fasta file description: Reference fasta file