From 010e7d09f302a0b0bc7e9d1f8359842c9a5813fd Mon Sep 17 00:00:00 2001
From: "Davi Marcon (@mxrcon)" <davijosuemarcon@gmail.com>
Date: Tue, 5 Apr 2022 22:41:51 -0300
Subject: [PATCH 1/5] Creating `download_gatk_jar.nf`

---
 modules/utils/download_gatk_jar.nf | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 modules/utils/download_gatk_jar.nf

diff --git a/modules/utils/download_gatk_jar.nf b/modules/utils/download_gatk_jar.nf
new file mode 100644
index 0000000..6f964e2
--- /dev/null
+++ b/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
+    """
+}

From 7ef56f1b68ae999c896da72414b531452629611f Mon Sep 17 00:00:00 2001
From: "Davi Marcon (@mxrcon)" <davijosuemarcon@gmail.com>
Date: Tue, 5 Apr 2022 22:48:24 -0300
Subject: [PATCH 2/5] adding a docker container for the module

---
 conf/docker.config | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/conf/docker.config b/conf/docker.config
index 436f017..ce96681 100644
--- a/conf/docker.config
+++ b/conf/docker.config
@@ -16,4 +16,8 @@ process {
         container = 'quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0'
     }
 
+    withName:
+    'DOWNLOAD_GATK_JAR' {
+        container = 'alpine:3.14'
+    }
 }

From b3463a941139a108b96f2b7c66f9a993d230a0c1 Mon Sep 17 00:00:00 2001
From: "Davi Marcon (@mxrcon)" <davijosuemarcon@gmail.com>
Date: Tue, 5 Apr 2022 22:59:06 -0300
Subject: [PATCH 3/5] adding `gatk_jar_link` to global params

---
 conf/global_params.config | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/conf/global_params.config b/conf/global_params.config
index bbaea5c..2784106 100644
--- a/conf/global_params.config
+++ b/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

From 0da326b709a08d0a0ba0f5193019c36e21c13594 Mon Sep 17 00:00:00 2001
From: "Davi Marcon (@mxrcon)" <davijosuemarcon@gmail.com>
Date: Wed, 6 Apr 2022 18:46:19 -0300
Subject: [PATCH 4/5] Adding `wget` and `tar` to conda env

---
 conda_envs/mtbseq-nf-env.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/conda_envs/mtbseq-nf-env.yml b/conda_envs/mtbseq-nf-env.yml
index 2afbf60..561009e 100644
--- a/conda_envs/mtbseq-nf-env.yml
+++ b/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

From 51c557b1f3c6fa92aa1d19045cc702d049efb3d3 Mon Sep 17 00:00:00 2001
From: "Davi Marcon (@mxrcon)" <davijosuemarcon@gmail.com>
Date: Sun, 10 Apr 2022 15:48:50 -0300
Subject: [PATCH 5/5] using the mtbseq container on `DOWNLOAD_GATK_JAR` process

---
 conf/docker.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/docker.config b/conf/docker.config
index ce96681..610c948 100644
--- a/conf/docker.config
+++ b/conf/docker.config
@@ -18,6 +18,6 @@ process {
 
     withName:
     'DOWNLOAD_GATK_JAR' {
-        container = 'alpine:3.14'
+        container = 'quay.io/biocontainers/mtbseq:1.0.3--pl526_1'
     }
 }