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Fix condition preventing to run multivcfanalyzer #711

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Merged
jfy133 merged 6 commits into from
Mar 29, 2021
Merged

Fix condition preventing to run multivcfanalyzer #711

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b1a132d
fix condition preventing to run multivcfanalyzer
maxibor Mar 24, 2021
6328dc4
update gatk_hc_out_mode
maxibor Mar 25, 2021
d11de6a
Merge branch 'dev' of github.com:nf-core/eager into dev
maxibor Mar 25, 2021
3814448
Merge branch 'dev' of github.com:nf-core/eager into dev
maxibor Mar 26, 2021
9c3b9ec
update changelog
maxibor Mar 26, 2021
1ca2fa9
Update CHANGELOG.md
jfy133 Mar 29, 2021
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- [#707](https://github.com/nf-core/eager/pull/707) - Fix typo in UnifiedGenotyper IndelRealigner command
- Fixed some Java tools not following process memory specifications
- Updated template to nf-core/tools 1.13.2
- - [#711](https://github.com/nf-core/eager/pull/711) - Fix conditional execution preventing multivcfanalyze to run

### `Dependencies`

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12 changes: 6 additions & 6 deletions main.nf
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Expand Up @@ -2494,22 +2494,22 @@ process vcf2genome {
// More complex consensus caller with additional filtering functionality (e.g. for heterozygous calls) to generate SNP tables and other things sometimes used in aDNA bacteria studies

// Create input channel for MultiVCFAnalyzer, possibly mixing with pre-made VCFs.
if (params.additional_vcf_files == '') {
ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it[7] }.collect()
if (!params.additional_vcf_files) {
ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it[-1] }.collect()
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} else {
ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it [7] }.collect().mix(ch_extravcfs_for_multivcfanalyzer)
ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it [-1] }.collect().mix(ch_extravcfs_for_multivcfanalyzer)
}

process multivcfanalyzer {
label 'mc_small'
publishDir "${params.outdir}/multivcfanalyzer", mode: params.publish_dir_mode

when:
params.genotyping_tool == 'ug' && params.run_multivcfanalyzer && params.gatk_ploidy == '2'
params.genotyping_tool == 'ug' && params.run_multivcfanalyzer && params.gatk_ploidy.toString() == '2'

input:
file vcf from ch_vcfs_for_multivcfanalyzer.collect()
file fasta from ch_fasta_for_multivcfanalyzer.collect()
file vcf from ch_vcfs_for_multivcfanalyzer
file fasta from ch_fasta_for_multivcfanalyzer

output:
file('fullAlignment.fasta.gz')
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