putz maxbin step as manual as the test data is too small

shaman-narayanasamy · Oct 13, 2016 · d36c680 · d36c680
1 parent 75e0726
commit d36c680
Showing 1 changed file with 158 additions and 156 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -20,160 +20,160 @@ before_script:
 
 # 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
-#
-#
-#
-#
-#
-# # PREPROCESSING
-# p-mgmt-default:
-#     stage: preprocessing
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -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 --single-step
-#
-#
-#
-# p-mgmt-nf:
-#     stage: preprocessing
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -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 --single-step
-#
-#
-# p-mg-default:
-#     stage: preprocessing
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -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 --single-step
-#
-#
-# p-mg-nf:
-#     stage: preprocessing
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -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 --single-step
-#
-#
-# p-mt-default:
-#     stage: preprocessing
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -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 --single-step
-#
-#
-# p-mt-nf:
-#     stage: preprocessing
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -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 --single-step
-#
-#
-# # Assembly
-# a-mgmt-idba:
-#     stage: manual
-#     when: manual
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly  -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
-#
-#
-# a-mg-idba:
-#     stage: manual
-#     when: manual
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly  -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
-#
-# a-mt-idba:
-#     stage: manual
-#     when: manual
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly  -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
-#
-# a-mgmt-megahit:
-#     stage: assembly
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
-#
-# a-mg-megahit:
-#     stage: assembly
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
-#
-#
-# a-mt-megahit:
-#     stage: assembly
-#     script:
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
-#
-#
-# an-mgmt:
-#     stage: analysis
-#     script:
-#         - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
-#         - cp -r /mnt/data/input/analysis-mgmt/* $CI_PROJECT_DIR/$CI_BUILD_ID
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db analysis --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
-#
-# an-mg:
-#     stage: analysis
-#     script:
-#         - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
-#         - cp -r /mnt/data/input/analysis-mg/* $CI_PROJECT_DIR/$CI_BUILD_ID
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db analysis --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
-#
-# an-mt:
-#     stage: analysis
-#     script:
-#         - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
-#         - cp -r /mnt/data/input/analysis-mt/* $CI_PROJECT_DIR/$CI_BUILD_ID
-#         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db analysis --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
+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
+
+
+
+
+
+# PREPROCESSING
+p-mgmt-default:
+    stage: preprocessing
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -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 --single-step
+
+
+
+p-mgmt-nf:
+    stage: preprocessing
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -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 --single-step
+
+
+p-mg-default:
+    stage: preprocessing
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -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 --single-step
+
+
+p-mg-nf:
+    stage: preprocessing
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -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 --single-step
+
+
+p-mt-default:
+    stage: preprocessing
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db preprocessing -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 --single-step
+
+
+p-mt-nf:
+    stage: preprocessing
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/no_filtering.conf.json -d /mnt/data/db preprocessing -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 --single-step
+
+
+# Assembly
+a-mgmt-idba:
+    stage: manual
+    when: manual
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly  -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
+
+
+a-mg-idba:
+    stage: manual
+    when: manual
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly  -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
+
+a-mt-idba:
+    stage: manual
+    when: manual
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a idba assembly  -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
+
+a-mgmt-megahit:
+    stage: assembly
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
+
+a-mg-megahit:
+    stage: assembly
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -m /mnt/data/input/assembly-megahit/mg.r1.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.r2.preprocessed.fq -m /mnt/data/input/assembly-megahit/mg.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
+
+
+a-mt-megahit:
+    stage: assembly
+    script:
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -a megahit assembly -t /mnt/data/input/assembly-megahit/mt.r1.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.r2.preprocessed.fq -t /mnt/data/input/assembly-megahit/mt.se.preprocessed.fq -o $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
+
+
+an-mgmt:
+    stage: analysis
+    script:
+        - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
+        - cp -r /mnt/data/input/analysis-mgmt/* $CI_PROJECT_DIR/$CI_BUILD_ID
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db analysis --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
+
+an-mg:
+    stage: analysis
+    script:
+        - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
+        - cp -r /mnt/data/input/analysis-mg/* $CI_PROJECT_DIR/$CI_BUILD_ID
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db analysis --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
+
+an-mt:
+    stage: analysis
+    script:
+        - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
+        - cp -r /mnt/data/input/analysis-mt/* $CI_PROJECT_DIR/$CI_BUILD_ID
+        - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db analysis --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step --single-omics
 
 
 # binny-mgmt:
@@ -192,14 +192,16 @@ before_script:
 
 
 maxbin-mgmt:
-    stage: binning
+    stage: manual
+    when: manual
     script:
         - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
         - cp -r /mnt/data/input/maxbin-mgmt/* $CI_PROJECT_DIR/$CI_BUILD_ID
         - impy -s . -c $CI_PROJECT_DIR/test/default.conf.json -d /mnt/data/db -b maxbin binning --data-dir $CI_PROJECT_DIR/$CI_BUILD_ID --single-step
 
 maxbin-mg:
-    stage: binning
+    stage: manual
+    when: manual
     script:
         - mkdir -p $CI_PROJECT_DIR/$CI_BUILD_ID
         - cp -r /mnt/data/input/maxbin-mg/* $CI_PROJECT_DIR/$CI_BUILD_ID