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update motus_downloaddb

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This commit is contained in:
JIANHONG OU 2022-04-17 11:22:23 -04:00
parent 32d5257def
commit 407d0bb752
2 changed files with 10 additions and 7 deletions
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7
modules/motus/downloaddb/main.nf
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@ -18,16 +18,17 @@ process MOTUS_DOWNLOADDB {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def software = ${motus_downloaddb.simpleName}_copy.py
""" """
## must copy file to working directory, ## must copy file to working directory,
## otherwise the reference_db will be download to bin folder ## otherwise the reference_db will be download to bin folder
## other than current directory ## other than current directory
cp $motus_downloaddb ${motus_downloaddb.simpleName}_copy.py cp $motus_downloaddb ${software}
python ${motus_downloaddb.simpleName}_copy.py \\ python ${software} \\
$args \\ $args \\
-t $task.cpus -t $task.cpus
## clean up ## clean up
rm ${motus_downloaddb.simpleName}_copy.py rm ${software}
## mOTUs version number is not available from command line. ## mOTUs version number is not available from command line.
## mOTUs save the version number in index database folder. ## mOTUs save the version number in index database folder.

6
modules/motus/downloaddb/meta.yml
View file

@ -5,6 +5,8 @@ keywords:
- metagenomics - metagenomics
- fastq - fastq
- taxonomic profiling - taxonomic profiling
- database
- download
tools: tools:
- "motus": - "motus":
description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data." description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data."
@ -19,7 +21,7 @@ input:
type: file type: file
description: | description: |
the mOTUs downloadDB script source file the mOTUs downloadDB script source file
pattern: "*{.py}" pattern: "downloadDB.py"
output: output:
- versions: - versions:
@ -27,7 +29,7 @@ output:
description: File containing software versions description: File containing software versions
pattern: "versions.yml" pattern: "versions.yml"
- db: - db:
type: file type: directory
description: The mOTUs database description: The mOTUs database
pattern: "db_mOTU" pattern: "db_mOTU"