[DEV] Adding a gatk_jar downloader

conda_envs/mtbseq-nf-env.yml

@@ -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

conf/docker.config

@@ -16,4 +16,8 @@ process {
         container = 'quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0'
     }
 
+    withName:
+    'DOWNLOAD_GATK_JAR' {
+        container = 'quay.io/biocontainers/mtbseq:1.0.3--pl526_1'
+    }
 }

conf/global_params.config

@@ -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"
+
 //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

modules/utils/download_gatk_jar.nf

@@ -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
+    """
+}