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[DEV] Adding a gatk_jar downloader #58

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[DEV] Adding a gatk_jar downloader #58

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010e7d0
Creating `download_gatk_jar.nf`
Mxrcon Apr 6, 2022
7ef56f1
adding a docker container for the module
Mxrcon Apr 6, 2022
b3463a9
adding `gatk_jar_link` to global params
Mxrcon Apr 6, 2022
0da326b
Adding `wget` and `tar` to conda env
Mxrcon Apr 6, 2022
51c557b
using the mtbseq container on `DOWNLOAD_GATK_JAR` process
Mxrcon Apr 10, 2022
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2 changes: 2 additions & 0 deletions conda_envs/mtbseq-nf-env.yml
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Expand Up @@ -7,3 +7,5 @@ dependencies:
- bioconda/linux-64::gatk=3.8.0
- bioconda::fastqc=0.11.9
- bioconda::multiqc=1.9
- conda-forge::wget=1.2
- conda-forge::tar=1.34
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4 changes: 4 additions & 0 deletions conf/docker.config
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Expand Up @@ -16,4 +16,8 @@ process {
container = 'quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0'
}

withName:
'DOWNLOAD_GATK_JAR' {
container = 'alpine:3.14'
}
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@Mxrcon , perhaps we might not need to use an extra container?

In these cases we can reuse (maybe?) the mtbseq container since its derived from debian and would be downloaded (and available) on the underlying machine anyhow.

What do you think?

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That's true, even alpine being a minimal container, we can use the mtbseq for it.

}
2 changes: 2 additions & 0 deletions conf/global_params.config
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Expand Up @@ -28,6 +28,8 @@ cohort_tsv = "${params.project}_cohort.tsv"

gatk38_jar = "${projectDir}/resources/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar"

gatk_jar_link = "https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2"

Comment on lines 29 to +32
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After some testing, preferably we can remove the necessity of gatk38_jar completely 🤔

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agreed, but we can keep it until we properly test it

//NOTE: Setting this OPTION will skip all filtering steps and report the calculated information for all positions in the input file.
// The all_vars only needs to be activated in MTBseq. But in mtbseq-nf we'll specify it as false
all_vars = false
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28 changes: 28 additions & 0 deletions modules/utils/download_gatk_jar.nf
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@@ -0,0 +1,28 @@
nextflow.enable.dsl = 2



params.gatk_jar_link = "https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2"

process DOWNLOAD_GATK_JAR {
publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish

output:
path('**/GenomeAnalysisTK.jar')


script:

"""
wget ${params.gatk_jar_link}
tar -xfv *.tar.bz2
"""

stub:

"""
echo "wget ${params.gatk_jar_link}"

touch GenomeAnalysisTK.jar
"""
}