uncomment DAG tests

.gitlab-ci.yml

@@ -33,60 +33,60 @@ i-with-another-filter:
 
 # DAG
 # see if the snakemake graph is resolving to the end
-# dag-mgmt-default:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
-#
-# dag-mgmt-maxbin:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -b maxbin -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
-#
-# dag-mgmt-idba:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -a idba -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
-#
-# dag-mgmt-nf:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
-#
-# dag-mgmt-nf2:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n" --no-filtering
-#
-# dag-mg-default:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
-#
-# dag-mg-nf:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
-#
-# dag-mg-nf2:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n" --no-filtering
-#
-# dag-mt-default:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
-#
-# dag-mt-nf:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
-#
-# dag-mt-nf2:
-#   stage: dag
-#   script:
-#     - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n" --no-filtering
+dag-mgmt-default:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
+
+dag-mgmt-maxbin:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -b maxbin -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
+
+dag-mgmt-idba:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -a idba -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
+
+dag-mgmt-nf:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n"
+
+dag-mgmt-nf2:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID -x "snakemake -n" --no-filtering
+
+dag-mg-default:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
+
+dag-mg-nf:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
+
+dag-mg-nf2:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -m $CI_PROJECT_DIR/test/MG.R1.small.fq -m $CI_PROJECT_DIR/test/MG.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n" --no-filtering
+
+dag-mt-default:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
+
+dag-mt-nf:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n"
+
+dag-mt-nf2:
+  stage: dag
+  script:
+    - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db run -t $CI_PROJECT_DIR/test/MT.R1.small.fq -t $CI_PROJECT_DIR/test/MT.R2.small.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-omics -x "snakemake -n" --no-filtering