From e7038eef112594728ad0ff620e0ba4b06fd77412 Mon Sep 17 00:00:00 2001
From: Davi Marcon <Davijosuemarcon@gmail.com>
Date: Wed, 24 Apr 2024 13:24:31 -0300
Subject: [PATCH] using biocontainers and removing custom container version
 (#85)

---
 conf/modules.config            |  2 +-
 container/Dockerfile           | 18 ------------------
 container/build_and_publish.sh | 33 ---------------------------------
 3 files changed, 1 insertion(+), 52 deletions(-)
 delete mode 100644 container/Dockerfile
 delete mode 100755 container/build_and_publish.sh

diff --git a/conf/modules.config b/conf/modules.config
index cfee07c..5f85f0d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -40,7 +40,7 @@ process {
     }
 
     withName: '.*TB.*' {
-        container = 'ghcr.io/mycobactopia-org/mtbseq-nf:0.9.7'
+        container = 'quay.io/biocontainers/mtbseq:1.1.0--hdfd78af_0'
 
     }
 
diff --git a/container/Dockerfile b/container/Dockerfile
deleted file mode 100644
index f3f2b4f..0000000
--- a/container/Dockerfile
+++ /dev/null
@@ -1,18 +0,0 @@
-FROM mambaorg/micromamba:0.25.1 AS base
-
-#NOTE: The conda env file has been copied via the build script
-COPY --chown=$MAMBA_USER:$MAMBA_USER mtbseq-nf-env.yml /tmp/mtbseq-nf-env.yml
-
-RUN micromamba create -n mtbseq-nf-env
-
-RUN micromamba install -y -n mtbseq-nf-env -f /tmp/mtbseq-nf-env.yml && micromamba clean -a -y
-
-FROM base AS condaenv
-
-ENV PATH /opt/conda/envs/mtbseq-nf-env/bin:$PATH
-
-COPY --chown=$MAMBA_USER:$MAMBA_USER GenomeAnalysisTK.jar /tmp/GenomeAnalysisTK.jar
-
-FROM condaenv AS gatkjar
-
-RUN /opt/conda/envs/mtbseq-nf-env/bin/gatk-register /tmp/GenomeAnalysisTK.jar
diff --git a/container/build_and_publish.sh b/container/build_and_publish.sh
deleted file mode 100755
index 9f5c274..0000000
--- a/container/build_and_publish.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env bash
-set -uex
-
-# NOTE: Make sure you've set the environment correctly and are logged in to the registry.
-# NOTE: Login to github registry with `echo $CR_PAT | docker login ghcr.io -u USERNAME --password-stdin`
-
-CONTAINER_TAG=0.9.7
-
-DOCKER_NAMESPACE="ghcr.io/mtb-bioinformatics"
-
-# NOTE: Do not embed the GATK jar inside the container since at process-level we already do gatk-register
-echo "Downloading and uncompressing GATK jar"
-wget "https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2"
-tar -xf GenomeAnalysisTK-3.8-0-ge9d806836.tar.bz2 --wildcards '*.jar'
-cp GenomeAnalysis*/*.jar .
-
-echo "Copying the mtbseq-nf-env file"
-cp ../conda_envs/mtbseq-nf-env.yml ./
-
-echo "Building mtbseq-nf container ..."
-CONTAINER_NAME=$DOCKER_NAMESPACE/"mtbseq-nf":$CONTAINER_TAG
-
-echo "Container Name : $CONTAINER_NAME "
-docker build -t $CONTAINER_NAME .
-CONTAINER_ID=$(docker run -d $CONTAINER_NAME)
-docker commit "$CONTAINER_ID" "$CONTAINER_NAME"
-docker stop "$CONTAINER_ID"
-docker push $DOCKER_NAMESPACE/"mtbseq-nf":$CONTAINER_TAG
-
-
-echo "Deleting the copied files"
-rm mtbseq-nf-env.yml
-rm -rf GenomeAnalysisTK*