fix checkm setup of DB and updated concoct/samtools version in conda

RVanDamme · Jul 22, 2020 · 1b31ee9 · 1b31ee9
1 parent c4c609a
commit 1b31ee9
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/configs/conda.config b/configs/conda.config
@@ -24,7 +24,7 @@ process {
     withLabel : maxbin2 { cpus = params.cpus ; memory = params.memory
             conda = 'bioconda::maxbin2=2.2.7'}
     withLabel : concoct { cpus = params.cpus ; memory = params.memory
-            conda = 'bioconda::concoct=1.1.0'}
+            conda = 'bioconda::samtools=1.10 bioconda::concoct=1.1.0'}
     withLabel : checkm { cpus = params.cpus ; memory = params.memory
             conda = 'bioconda::checkm-genome=1.0.13'}
     withLabel : metawrap { cpus = params.cpus ; memory = params.memory;

diff --git a/modules/checkmsetupDB.nf b/modules/checkmsetupDB.nf
@@ -18,7 +18,7 @@ process checkm_setup_db {
                     path_db=\$(dirname !{db});
                     mkdir -p \$path_db/db/;
                     tar -xvf ${db} -C \$path_db/db/;
-                    checkm data setRoot \$path_db/db;   
+                    echo -e "cat << EOF\\n\$path_db/db\\nEOF\\n" | checkm data setRoot   
                     echo \$path_db/db > path_db.txt;
         fi
         """