From 1c7205d68389a899ee6b4f8c11343701c2c07ce8 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 6 May 2022 10:44:51 +0200
Subject: [PATCH] fixed container definitions

---
 modules/md5sum/main.nf | 8 ++++----
 modules/shasum/main.nf | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules/md5sum/main.nf b/modules/md5sum/main.nf
index 2cdb8bf6..7b66625e 100644
--- a/modules/md5sum/main.nf
+++ b/modules/md5sum/main.nf
@@ -2,10 +2,10 @@ process MD5SUM {
     tag "$meta.id"
     label 'process_low'
 
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using md5sum. Please use docker or singularity containers."
-    }
-    container "debian:bullseye-slim"
+    conda (params.enable_conda ? "conda-forge::coreutils=8.25" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/coreutils:8.31--h14c3975_0' :
+        'quay.io/biocontainers/coreutils:8.31--h14c3975_0' }"
 
     input:
     tuple val(meta), path(file)
diff --git a/modules/shasum/main.nf b/modules/shasum/main.nf
index e7a18da6..11f9376c 100644
--- a/modules/shasum/main.nf
+++ b/modules/shasum/main.nf
@@ -2,10 +2,10 @@ process SHASUM {
     tag "$meta.id"
     label 'process_low'
 
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using sha256sum. Please use docker or singularity containers."
-    }
-    container "debian:bullseye-slim"
+    conda (params.enable_conda ? "conda-forge::coreutils=8.25" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/coreutils:8.31--h14c3975_0' :
+        'quay.io/biocontainers/coreutils:8.31--h14c3975_0' }"
 
     input:
     tuple val(meta), path(file)