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Fix kraken2 module

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This commit is contained in:
James Fellows Yates 2022-03-28 16:46:45 +02:00
parent 231253227c
commit 98dc8014a5
2 changed files with 5 additions and 6 deletions
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6
modules.json
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@ -24,11 +24,11 @@
"multiqc": { "multiqc": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },
"untar": {
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
},
"porechop": { "porechop": {
"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046" "git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
},
"untar": {
"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
} }
} }
} }

3
modules/nf-core/modules/kraken2/kraken2/main.nf generated
View file

@ -32,13 +32,12 @@ process KRAKEN2_KRAKEN2 {
--threads $task.cpus \\ --threads $task.cpus \\
--unclassified-out $unclassified \\ --unclassified-out $unclassified \\
--classified-out $classified \\ --classified-out $classified \\
$args \\
--report ${prefix}.kraken2.report.txt \\ --report ${prefix}.kraken2.report.txt \\
--gzip-compressed \\ --gzip-compressed \\
$paired \\ $paired \\
$args \\
$reads $reads
pigz -p $task.cpus *.fastq pigz -p $task.cpus *.fastq
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml