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epang: Output gzipped jplace (#2037)

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* Output gzipped jplace
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Daniel Lundin 2022-09-09 09:54:03 +02:00 committed by GitHub
parent 4f78d40b11
commit e97d4cd32b
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3 changed files with 8 additions and 5 deletions
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7
modules/epang/main.nf
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@ -45,8 +45,11 @@ process EPANG {
$splitarg \\ $splitarg \\
$binaryarg $binaryarg
[ -e epa_result.jplace ] && mv epa_result.jplace ${prefix}.epa_result.jplace if [ -e epa_result.jplace ]; then
[ -e epa_info.log ] && mv epa_info.log ${prefix}.epa_info.log gzip epa_result.jplace
cp epa_result.jplace.gz ${prefix}.epa_result.jplace.gz
fi
[ -e epa_info.log ] && cp epa_info.log ${prefix}.epa_info.log
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

4
modules/epang/meta.yml
View file

@ -55,8 +55,8 @@ output:
description: directory in which EPA-NG was run description: directory in which EPA-NG was run
- jplace: - jplace:
type: file type: file
description: file with placement information description: gzipped file with placement information
pattern: "*.jplace" pattern: "*.jplace.gz"
- log: - log:
type: file type: file
description: log file from placement description: log file from placement

2
tests/modules/epang/test.yml
View file

@ -6,7 +6,7 @@
- path: output/epang/test.epa_info.log - path: output/epang/test.epa_info.log
contains: contains:
- "INFO 3 Sequences done" - "INFO 3 Sequences done"
- path: output/epang/test.epa_result.jplace - path: output/epang/test.epa_result.jplace.gz
contains: contains:
- '"placements":' - '"placements":'
- '"metadata": {"invocation": "epa-ng --model LG --threads 2 --query query.alnfaa.gz --ref-msa reference.alnfaa.gz --tree reference.newick "}' - '"metadata": {"invocation": "epa-ng --model LG --threads 2 --query query.alnfaa.gz --ref-msa reference.alnfaa.gz --tree reference.newick "}'