diff --git a/.github/workflows/workflow_modules.yml b/.github/workflows/workflow_modules.yml
index 74c9423d..3564777e 100644
--- a/.github/workflows/workflow_modules.yml
+++ b/.github/workflows/workflow_modules.yml
@@ -91,7 +91,9 @@ jobs:
           " --databases=/vol/scratch/databases/      " \
           ./example_params/fullPipelineONT.yml "${WORK_DIR}" \
           ${PROFILE} ${VERSION}  || exit 1
-
+      - name: Cleanup previous checkm results for correct aggregation run
+        run: |
+          rm -rf output
       - name: Test Full Pipeline ONT and Illumina Run
         run: |
           VERSION=$(sort -r VERSIONS.txt | tail -n 1)
@@ -120,6 +122,16 @@ jobs:
     runs-on: [ self-hosted, slurm]
     steps:
       - uses: actions/checkout@v2
+      - name: Set Secrets
+        run: |
+          make set_secrets SECRET_NAME=S3_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
+          make set_secrets SECRET_NAME=S3_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
+          make set_secrets SECRET_NAME=S3_checkm_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
+          make set_secrets SECRET_NAME=S3_checkm_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
+          make set_secrets SECRET_NAME=S3_checkm2_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
+          make set_secrets SECRET_NAME=S3_checkm2_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
+          make set_secrets SECRET_NAME=S3_gtdb_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
+          make set_secrets SECRET_NAME=S3_gtdb_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
       - name: Test MAG Attributes
         run: |
           bash ./scripts/test_magAttributes.sh \
@@ -131,17 +143,7 @@ jobs:
           bash ./scripts/test_magAttributes.sh \
           " --databases=/vol/scratch/databases/    " \
           example_params/magAttributes_fraction/magAttributes.yml "${WORK_DIR}" ${PROFILE} || exit 1
-      - name: Set Secrets
-        run: |
-          make set_secrets SECRET_NAME=S3_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
-          make set_secrets SECRET_NAME=S3_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
-          make set_secrets SECRET_NAME=S3_checkm_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
-          make set_secrets SECRET_NAME=S3_checkm_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
-          make set_secrets SECRET_NAME=S3_gtdb_ACCESS SECRET_VALUE=${{ secrets.S3_ACCESS }}
-          make set_secrets SECRET_NAME=S3_gtdb_SECRET SECRET_VALUE=${{ secrets.S3_VALUE }}
-
-
-      - name: Test Checkm runs against different database parameters
+      - name: Test Checkm1 runs against different database parameters
         run: |
           make runDatabaseTest MODULE_DB_TEST_EXTRACTED="/vol/spool/toolkit/checkm/" \
                                MODULE_DB_TEST_MD5SUM="0963b301dfe9345ea4be1246e32f6728" \
@@ -149,11 +151,26 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/checkm_data_2015_01_16.tar.gz" MODULE_DB_TEST_S3PATH="s3://databases/checkm_data_2015_01_16.tar.gz" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/checkm/*"  \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/checkm \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/checkm \
                                MODULE_DB_TEST_YML=example_params/magAttributes.yml \
-                               MODULE_DB_TEST_YML_PATH="'.steps.magAttributes.checkm.database=env(database),del(.steps.magAttributes.gtdb,.steps.magAttributes.prokka)'" \
+                               MODULE_DB_TEST_YML_PATH="'.steps.magAttributes.checkm.database=env(database),del(.steps.magAttributes.gtdb,.steps.magAttributes.checkm2,.steps.magAttributes.prokka)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_magAttributes.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/checkm_yaml_database_tests" \
                                MODULE_DB_TEST_REMOVE_DB="yes"
+
+      - name: Test Checkm2 runs against different database parameters
+        run: |
+          make runDatabaseTest MODULE_DB_TEST_EXTRACTED="/vol/spool/toolkit/checkm2/" \
+                               MODULE_DB_TEST_MD5SUM="a634cb3d31a1f56f2912b74005f25f09" \
+                               MODULE_DB_TEST_HTTPS="https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm2_v2.tar.gz" \
+                               MODULE_DB_TEST_PATH="/vol/spool/toolkit/checkm2_v2.tar.gz" MODULE_DB_TEST_S3PATH="s3://databases/checkm2_v2.tar.gz" \
+                               MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/checkm2/*"  \
+                               MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/checkm2 \
+                               MODULE_DB_TEST_YML=example_params/magAttributes.yml \
+                               MODULE_DB_TEST_YML_PATH="'.steps.magAttributes.checkm2.database=env(database),del(.steps.magAttributes.gtdb,.steps.magAttributes.checkm,.steps.magAttributes.prokka)'" \
+                               MODULE_DB_TEST_YML_SCRIPT="./scripts/test_magAttributes.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/checkm2_yaml_database_tests" \
+                               MODULE_DB_TEST_REMOVE_DB="yes"
+ 
       
       - name: Test GTDB runs against different database parameters
         run: |
@@ -163,9 +180,10 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/gtdbtk_r214_data.tar.gz" MODULE_DB_TEST_S3PATH="s3://databases/gtdbtk_r214_data.tar.gz" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/gtdbtk_r214_data/*" \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/gtdb \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials \
+                               MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/gtdb \
                                MODULE_DB_TEST_YML=example_params/magAttributes.yml \
-                               MODULE_DB_TEST_YML_PATH="'.steps.magAttributes.gtdb.database=env(database),del(.steps.magAttributes.checkm,.steps.magAttributes.prokka)'" \
+                               MODULE_DB_TEST_YML_PATH="'.steps.magAttributes.gtdb.database=env(database),del(.steps.magAttributes.checkm,.steps.magAttributes.checkm2,.steps.magAttributes.prokka)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_magAttributes.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/gtdb_yaml_database_tests"  \
                                MODULE_DB_TEST_REMOVE_DB="yes"
 
@@ -296,7 +314,8 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/card_20221209.tar.bz2" MODULE_DB_TEST_S3PATH="s3://databases/card_20221209.tar.bz2" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/card_20221209/*" \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/rgi \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials \
+                               MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/rgi \
                                MODULE_DB_TEST_YML=example_params/annotation.yml \
                                MODULE_DB_TEST_YML_PATH="'.steps.annotation.rgi.database=env(database),del(.steps.annotation.mmseqs2,.steps.annotation.keggFromBlast)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_annotation.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/rgi_yaml_database_tests" \
@@ -311,7 +330,8 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/kegg.tar.gz" MODULE_DB_TEST_S3PATH="s3://databases_internal/kegg-links-mirror-2021-01.tar.gz" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases_internal/kegg-links-mirror-2021-01/*"  \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/kegg \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials \
+                               MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/kegg \
                                MODULE_DB_TEST_YML=example_params/annotation.yml \
                                MODULE_DB_TEST_YML_PATH="'.steps.annotation.keggFromBlast.database=env(database),del(.steps.annotation.rgi)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_annotation.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/kegg_yaml_database_tests" \
@@ -339,7 +359,8 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/kegg-mirror-2021-01_mmseqs.tar.zst" MODULE_DB_TEST_S3PATH="s3://databases_internal/kegg-mirror-2021-01_mmseqs.tar.zst" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases_internal/kegg-mirror-2021-01_mmseqs/*" \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/mmseqs2 \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials \
+                               MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/mmseqs2 \
                                MODULE_DB_TEST_YML=example_params/annotation.yml \
                                MODULE_DB_TEST_YML_PATH="'.steps.annotation.mmseqs2.kegg.database=env(database),del(.steps.annotation.rgi,.steps.annotation.keggFromBlast)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_annotation.sh" \
@@ -387,7 +408,8 @@ jobs:
                                MODULE_DB_TEST_S3PATH="s3://databases/plasmids_plsdb_20220929.tar.bz2" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/plasmids_plsdb_20220929/*" \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/plasmids \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials \
+                               MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/plasmids \
                                MODULE_DB_TEST_YML=example_params/plasmid.yml MODULE_DB_TEST_YML_PATH="'.steps.plasmid.PLSDB.database=env(database),del(.steps.plasmid.Platon,.steps.plasmid.ViralVerifyPlasmid,.steps.plasmid.MobTyper)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_plasmids.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/plasmid_yaml_database_tests" \
                                MODULE_DB_TEST_REMOVE_DB="yes"
@@ -399,7 +421,7 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/pfam-A_35.0.hmm.gz" MODULE_DB_TEST_S3PATH="s3://databases/pfam-A_35.0.hmm.gz" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/pfam-A_35.*.hmm" \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl  --no-sign-request  --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/plasmids MODULE_DB_TEST_YML=example_params/plasmid.yml \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/plasmids MODULE_DB_TEST_YML=example_params/plasmid.yml \
                                MODULE_DB_TEST_YML_PATH="'.steps.plasmid.ViralVerifyPlasmid.database=env(database),del(.steps.plasmid.Platon,.steps.plasmid.PlasClass,.steps.plasmid.MobTyper,.steps.plasmid.PLSDB)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_plasmids.sh" \
                                MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/plasmid_yaml_database_tests" \
@@ -413,7 +435,7 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/platon_20220929.tar.gz" MODULE_DB_TEST_S3PATH="s3://databases/platon_20220929.tar.gz" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/platon/*" \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl  --no-sign-request  --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/plasmids MODULE_DB_TEST_YML=example_params/plasmid.yml \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/plasmids MODULE_DB_TEST_YML=example_params/plasmid.yml \
                                MODULE_DB_TEST_YML_PATH="'.steps.plasmid.Platon.database=env(database),del(.steps.plasmid.ViralVerifyPlasmid,.steps.plasmid.PlasClass,.steps.plasmid.MobTyper,.steps.plasmid.PLSDB)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_plasmids.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/plasmid_yaml_database_tests" \
                                MODULE_DB_TEST_REMOVE_DB="yes"
@@ -426,7 +448,7 @@ jobs:
                                MODULE_DB_TEST_PATH="/vol/spool/toolkit/mob_20220929.gz" MODULE_DB_TEST_S3PATH="s3://databases/mob_20220929.gz" \
                                MODULE_DB_TEST_S3_DIRECTORY_PATH="s3://databases/mob_20220929/*" \
                                MODULE_DB_TEST_S5CMD_COMMAND='" --retry-count 30 --no-verify-ssl  --no-sign-request  --endpoint-url https://openstack.cebitec.uni-bielefeld.de:8080 "' \
-                               MODULE_DB_TEST_GENERATED_YML=/vol/spool/generated_yamls/plasmids MODULE_DB_TEST_YML=example_params/plasmid.yml \
+                               MODULE_DB_TEST_CREDENTIALS=/vol/spool/credentials MODULE_DB_TEST_GENERATED_YML=${WORK_DIR}/generated_yamls/plasmids MODULE_DB_TEST_YML=example_params/plasmid.yml \
                                MODULE_DB_TEST_YML_PATH="'.steps.plasmid.MobTyper.database=env(database),del(.steps.plasmid.ViralVerifyPlasmid,.steps.plasmid.PlasClass,.steps.plasmid.Platon,.steps.plasmid.PLSDB)'" \
                                MODULE_DB_TEST_YML_SCRIPT="./scripts/test_plasmids.sh" MODULE_DB_TEST_GENERATED_YML_DIR="${WORK_DIR}/plasmid_yaml_database_tests" \
                                MODULE_DB_TEST_REMOVE_DB="yes"
diff --git a/bin/emgb.sh b/bin/emgb.sh
index 685627de..f78806cc 100755
--- a/bin/emgb.sh
+++ b/bin/emgb.sh
@@ -79,7 +79,7 @@ function getContigs {
 
 
 function getBins {
-	checkm=$(find $OUTPUT_PATH/$RUN_ID/magAttributes/*/checkm/ -name "*_checkm_*.tsv" -exec readlink -f {} \; | sed 's/^/ -checkm-tsv /g')
+	checkm=$(find $OUTPUT_PATH/$RUN_ID/magAttributes/*/checkm*/ -name "*_checkm*_*.tsv" -exec readlink -f {} \; | sed 's/^/ -checkm-tsv /g')
 	gtdbtk=$(find $OUTPUT_PATH/$RUN_ID/magAttributes/*/gtdb/ -name "*.summary.tsv" -exec readlink -f {} \; | sed 's/^/ -gtdbtk-tsvs /g')
 	bins=$(find $BINS_DIR -name "*_bin.*.fa" -exec readlink -f {} \; | tail -n 1 | rev | cut -f 1 -d '/' | rev | cut -d '.' -f 1 | sed 's/^/  -bin-id-prefix /g')
 	json=" -json-gz $(pwd)/${NAME}.bins.json.gz "
diff --git a/default/fullPipeline_illumina_nanpore.yml b/default/fullPipeline_illumina_nanpore.yml
index 241dc490..b2add82a 100644
--- a/default/fullPipeline_illumina_nanpore.yml
+++ b/default/fullPipeline_illumina_nanpore.yml
@@ -101,18 +101,12 @@ steps:
           source: https://openstack.cebitec.uni-bielefeld.de:8080/databases/gtdbtk_r214_data.tar.gz
           md5sum: 390e16b3f7b0c4463eb7a3b2149261d9
       additionalParams: " --min_af 0.65 --scratch_dir . "
-    # checkm lineage_wf
-    checkm:
+    checkm2:
       database:
         download:
-                # Use Version number in databse names
-          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm_data_2015_01_16.tar.gz"
-          md5sum: 0963b301dfe9345ea4be1246e32f6728
-      buffer: 200
-      additionalParams:
-        tree: " --reduced_tree "
-        lineage_set: " " 
-        qa: "  "
+          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm2_v2.tar.gz"
+          md5sum: a634cb3d31a1f56f2912b74005f25f09
+      additionalParams: "  "
   fragmentRecruitment:
     mashScreen:
       genomes: test_data/fragmentRecruitment/mags.tsv
diff --git a/default/fullPipeline_illumina_nanpore_without_aggregate.yml b/default/fullPipeline_illumina_nanpore_without_aggregate.yml
index d2213731..caafd586 100644
--- a/default/fullPipeline_illumina_nanpore_without_aggregate.yml
+++ b/default/fullPipeline_illumina_nanpore_without_aggregate.yml
@@ -101,18 +101,12 @@ steps:
           source: https://openstack.cebitec.uni-bielefeld.de:8080/databases/gtdbtk_r214_data.tar.gz
           md5sum: 390e16b3f7b0c4463eb7a3b2149261d9
       additionalParams: " --min_af 0.65 --scratch_dir . "
-    # checkm lineage_wf
-    checkm:
+    checkm2:
       database:
         download:
-                # Use Version number in databse names
-          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm_data_2015_01_16.tar.gz"
-          md5sum: 0963b301dfe9345ea4be1246e32f6728
-      buffer: 200
-      additionalParams:
-        tree: " --reduced_tree "
-        lineage_set: " " 
-        qa: "  "
+          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm2_v2.tar.gz"
+          md5sum: a634cb3d31a1f56f2912b74005f25f09
+      additionalParams: "  "
   fragmentRecruitment:
     mashScreen:
       genomes: test_data/fragmentRecruitment/mags.tsv
diff --git a/docker/toolkit-checkm2/Dockerfile b/docker/toolkit-checkm2/Dockerfile
new file mode 100644
index 00000000..76ace6ea
--- /dev/null
+++ b/docker/toolkit-checkm2/Dockerfile
@@ -0,0 +1,14 @@
+FROM ubuntu:focal
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update \
+    && apt install -y git python3-pip prodigal diamond-aligner wget \
+    && pip3 install setuptools wheel requests packaging tqdm \    
+    && pip3 install protobuf==3.20.* scikit-learn==0.23.2 h5py==2.10.0 numpy==1.19.2 tensorflow==2.5.0 lightgbm==3.2.1 pandas==1.4.0 scipy==1.8.0
+
+ENV CHECKM2_VERSION=1.0.2
+
+RUN git clone -b $CHECKM2_VERSION --recursive https://github.com/chklovski/checkm2.git && cd checkm2 \
+    && python3 setup.py install
+
+ENV PATH="$HOME/.local/bin:$PATH"
diff --git a/docker/toolkit-checkm2/VERSION b/docker/toolkit-checkm2/VERSION
new file mode 100644
index 00000000..446dec6f
--- /dev/null
+++ b/docker/toolkit-checkm2/VERSION
@@ -0,0 +1 @@
+1.0.2-1
diff --git a/docs/modules/magAttributes.md b/docs/modules/magAttributes.md
index 272929c2..9c4a1eec 100644
--- a/docs/modules/magAttributes.md
+++ b/docs/modules/magAttributes.md
@@ -49,7 +49,8 @@ nextflow secrets set S3_checkm_SECRET XXXXXXX
 All GTDB files include the GTDB specific columns in addition to a `SAMPLE` column (`SAMPLE_gtdbtk.bac120.summary.tsv`, `SAMPLE_gtdbtk.ar122.summary.tsv`).
 In addition, this module produces a file `SAMPLE_gtdbtk_CHUNK.tsv` that combines both files and adds a `BIN_ID` column that adheres to the magAttributes specification
 
-### Checkm
+### Checkm and Checkm2
 
-The Checkm output adheres to the magAttributes specification and adds a `BIN_ID` and `SAMPLE` column to the output file.
+The Checkm and Checkm2 output adheres to the magAttributes specification and adds a `BIN_ID` and `SAMPLE` column to the output file.
+If Checkm2 and Checkm are both specified in the config file then only the Checkm2 results are used for downstream pipeline steps.
 
diff --git a/example_params/fullPipeline.yml b/example_params/fullPipeline.yml
index 285b83eb..82ca090d 100644
--- a/example_params/fullPipeline.yml
+++ b/example_params/fullPipeline.yml
@@ -53,16 +53,12 @@ steps:
           source: https://openstack.cebitec.uni-bielefeld.de:8080/databases/gtdbtk_r214_data.tar.gz
           md5sum: 390e16b3f7b0c4463eb7a3b2149261d9
       additionalParams: " --min_af 0.65 --scratch_dir . "
-    checkm:
+    checkm2:
       database:
         download:
-          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm_data_2015_01_16.tar.gz"
-          md5sum: 0963b301dfe9345ea4be1246e32f6728
-      buffer: 200
-      additionalParams:
-        tree: " --reduced_tree "
-        lineage_set: " " 
-        qa: "  "
+          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm2_v2.tar.gz"
+          md5sum: a634cb3d31a1f56f2912b74005f25f09
+      additionalParams: "  "
   fragmentRecruitment:
     mashScreen:
       genomes: test_data/fragmentRecruitment/mags.tsv
diff --git a/example_params/fullPipelineIlluminaOrONT.yml b/example_params/fullPipelineIlluminaOrONT.yml
index 99ec6618..5e44a4b8 100644
--- a/example_params/fullPipelineIlluminaOrONT.yml
+++ b/example_params/fullPipelineIlluminaOrONT.yml
@@ -92,16 +92,12 @@ steps:
           source: https://openstack.cebitec.uni-bielefeld.de:8080/databases/gtdbtk_r214_data.tar.gz
           md5sum: 390e16b3f7b0c4463eb7a3b2149261d9
       additionalParams: " --min_af 0.65 --scratch_dir . "
-    checkm:
+    checkm2:
       database:
         download:
-          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm_data_2015_01_16.tar.gz"
-          md5sum: 0963b301dfe9345ea4be1246e32f6728
-      buffer: 200
-      additionalParams:
-        tree: " --reduced_tree "
-        lineage_set: " " 
-        qa: "  "
+          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm2_v2.tar.gz"
+          md5sum: a634cb3d31a1f56f2912b74005f25f09
+      additionalParams: "  "
   dereplication:
     bottomUpClustering:
       minimumCompleteness: 0
diff --git a/example_params/magAttributes.yml b/example_params/magAttributes.yml
index 430c3dbf..9aca6b1b 100644
--- a/example_params/magAttributes.yml
+++ b/example_params/magAttributes.yml
@@ -17,6 +17,12 @@ steps:
           source: https://openstack.cebitec.uni-bielefeld.de:8080/databases/gtdbtk_r214_data.tar.gz
           md5sum: 390e16b3f7b0c4463eb7a3b2149261d9
       additionalParams: " --min_af 0.65 --scratch_dir . "
+    checkm2:
+      database:
+        download:
+          source: "https://openstack.cebitec.uni-bielefeld.de:8080/databases/checkm2_v2.tar.gz"
+          md5sum: a634cb3d31a1f56f2912b74005f25f09
+      additionalParams: "  "
     checkm:
       database:
         download:
diff --git a/main.nf b/main.nf
index 923b1c85..43381ab3 100644
--- a/main.nf
+++ b/main.nf
@@ -328,6 +328,18 @@ workflow wAggregatePipeline {
      | map { sra, bins -> bins} \
      | set { checkm }
 
+    // get Checkm2 results
+    Pattern checkm2Pattern = Pattern.compile('.*/magAttributes/' + params.modules.magAttributes.version.major + '..*/.*/.*_checkm2_.*.tsv$')
+     selectedSRAMagAttributes | filter({ sra, path -> checkm2Pattern.matcher(path.toString()).matches()}) \
+     | splitCsv(header: true, sep: '\t') \
+     | map { sra, bins -> bins} \
+     | set { checkm2 }
+
+    // We allow only to execute checkm or checkm2 but not both
+    checkm \
+       | mix(checkm2) \
+       | set {checkm}
+
     // get gtdbtk summary files
     Pattern gtdbPattern = Pattern.compile('.*/magAttributes/' + params.modules.magAttributes.version.major + '..*/.*/.*_gtdbtk_combined.tsv$' )
     selectedSRAMagAttributes | filter({ sra, path -> gtdbPattern.matcher(path.toString()).matches()}) \
diff --git a/modules/magAttributes/module.nf b/modules/magAttributes/module.nf
index 616e532a..3ef880e1 100644
--- a/modules/magAttributes/module.nf
+++ b/modules/magAttributes/module.nf
@@ -46,7 +46,8 @@ process pCheckM {
     publishDir params.output, mode: "${params.publishDirMode}", saveAs: { filename -> getOutput("${sample}", params.runid, "checkm", filename) }, \
       pattern: "{**.tsv}"
 
-    when params.steps.containsKey("magAttributes") && params.steps.magAttributes.containsKey("checkm")
+    when params.steps.containsKey("magAttributes") && params.steps.magAttributes.containsKey("checkm") \
+	&& !params.steps.magAttributes.containsKey("checkm2")
 
     containerOptions Utils.getDockerMount(params.steps?.magAttributes?.checkm?.database, params) 
 
@@ -74,6 +75,44 @@ process pCheckM {
 }
 
 
+process pCheckM2 {
+
+    container "${params.checkm2_image}"
+
+    tag "Sample: $sample"
+
+    secret { "${S3_checkm2_ACCESS}"!="" ? ["S3_checkm2_ACCESS", "S3_checkm2_SECRET"] : [] } 
+
+    publishDir params.output, mode: "${params.publishDirMode}", saveAs: { filename -> getOutput("${sample}", params.runid, "checkm2", filename) }, \
+      pattern: "{**.tsv}"
+
+    when params.steps.containsKey("magAttributes") && params.steps.magAttributes.containsKey("checkm2")
+
+    containerOptions Utils.getDockerMount(params.steps?.magAttributes?.checkm2?.database, params)
+
+    beforeScript "mkdir -p ${params.polished.databases}"
+
+    label 'medium'
+
+    input:
+    tuple val(sample), val(ending), path(bins) 
+
+    output:
+    tuple path("${sample}_checkm2_*.tsv", type: "file"), val("${sample}"), emit: checkm
+    tuple env(FILE_ID), val("${output}"), val(params.LOG_LEVELS.INFO), file(".command.sh"), \
+	file(".command.out"), file(".command.err"), file(".command.log"), emit: logs
+
+    shell:
+    output = getOutput("${sample}", params.runid, "checkm2", "")
+    S5CMD_PARAMS=params?.steps?.magAttributes?.checkm2?.database?.download?.s5cmd?.params ?: "" 
+    DOWNLOAD_LINK=params?.steps?.magAttributes?.checkm2?.database?.download?.source ?: ""
+    MD5SUM=params.steps?.magAttributes?.checkm2?.database?.download?.md5sum ?: ""
+    EXTRACTED_DB=params.steps?.magAttributes?.checkm2?.database?.extractedDBPath ?: ""
+    S3_checkm2_ACCESS=params?.steps?.magAttributes?.checkm2?.database?.download?.s5cmd && S5CMD_PARAMS.indexOf("--no-sign-request") == -1 ? "\$S3_checkm2_ACCESS" : ""
+    S3_checkm2_SECRET=params?.steps?.magAttributes?.checkm2?.database?.download?.s5cmd && S5CMD_PARAMS.indexOf("--no-sign-request") == -1 ? "\$S3_checkm2_SECRET" : ""
+    template 'checkm2.sh'
+}
+
 process pGtdbtk {
 
     container "${params.gtdbtk_image}"
@@ -249,6 +288,7 @@ workflow _wMagAttributes {
    main:
      GTDB_DEFAULT_BUFFER = 500
      CHECKM_DEFAULT_BUFFER = 30
+     CHECKM2_DEFAULT_BUFFER = 20000
      BIN_FILES_INPUT_IDX = 1
 
      DATASET_IDX = 0
@@ -261,18 +301,22 @@ workflow _wMagAttributes {
      // get file ending of bin files (.fa, .fasta, ...) and group by file ending and dataset
      bins | flatMap({n -> groupBins(n, params?.steps?.magAttributes?.checkm?.buffer ?: CHECKM_DEFAULT_BUFFER)}) \
        | pCheckM | set {checkm}
+     bins | flatMap({n -> groupBins(n, params?.steps?.magAttributes?.checkm2?.buffer ?: CHECKM2_DEFAULT_BUFFER)}) \
+       | pCheckM2 | set { checkm2 }
      bins | flatMap({n -> groupBins(n, params?.steps?.magAttributes?.gtdb?.buffer ?: GTDB_DEFAULT_BUFFER )}) \
        | pGtdbtk | set {gtdb}
 
-     // Prepare checkm output file
-     checkm.checkm | groupTuple(by: DATASET_OUTPUT_IDX, remainder: true) | map { it -> it[BIN_FILES_OUTPUT_GROUP_IDX] }  | flatten | map { bin -> file(bin) } \
+     checkm2.checkm | mix(checkm.checkm) | set {checkmSelected}
+
+     // Prepare checkm2 output file
+     checkmSelected | groupTuple(by: DATASET_OUTPUT_IDX, remainder: true) | map { it -> it[BIN_FILES_OUTPUT_GROUP_IDX] }  | flatten | map { bin -> file(bin) } \
        | collectFile(keepHeader: true, newLine: false ){ item -> [ "bin_attributes.tsv", item.text ] } \
        | splitCsv(sep: '\t', header: true) \
-       | set{ checkm_list } 
+       | set{ checkmSelectedList } 
 
      if(params.summary){
-       // collect checkm files for checkm results across multiple datasets
-       checkm.checkm \
+       // collect checkm files for checkm2 results across multiple datasets
+       checkmSelected \
           | collectFile(newLine: false, keepHeader: true, storeDir: params.output + "/summary/"){ item ->
          [ "checkm.tsv", item[BIN_FILES_OUTPUT_IDX].text  ]
        }
@@ -290,6 +334,6 @@ workflow _wMagAttributes {
      pGtdbtk.out.logs | mix(pCheckM.out.logs) | pDumpLogs 
 
    emit:
-     checkm = checkm_list
+     checkm = checkmSelectedList
      gtdb = gtdb.combined
 }
diff --git a/nextflow.config b/nextflow.config
index c85ffe5c..a49ab00f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -282,6 +282,7 @@ params {
    maxbin_image = "quay.io/biocontainers/maxbin2:2.2.7--he1b5a44_2"
    gtdbtk_image = "quay.io/metagenomics/toolkit-gtdbtk:2.1.1-2"
    checkm_image = "quay.io/metagenomics/toolkit-checkm:0.1.0"
+   checkm2_image = "quay.io/metagenomics/toolkit-checkm2:1.0.2-1"
    prokka_image = "quay.io/metagenomics/toolkit-prokka:1.14.6-1"
    fastp_image = "quay.io/biocontainers/fastp:0.23.2--h79da9fb_0"
    nanoplot_image = "quay.io/biocontainers/nanoplot:1.40.0--pyhdfd78af_0"
diff --git a/templates/checkm2.sh b/templates/checkm2.sh
new file mode 100644
index 00000000..689686a4
--- /dev/null
+++ b/templates/checkm2.sh
@@ -0,0 +1,53 @@
+
+# Prepare checkm patch, output directory and output file name
+mkdir out
+FILE_ID=$(mktemp XXXXXXXX)
+OUTPUT=!{sample}_checkm2_${FILE_ID}.tsv
+
+# Check developer documentation
+if [ -z "!{EXTRACTED_DB}" ]
+then
+  DATABASE=!{params.polished.databases}/checkm2
+  LOCK_FILE=${DATABASE}/lock.txt
+
+  if [ ! -z "!{S3_checkm2_ACCESS}" ]
+  then
+    export AWS_ACCESS_KEY_ID=!{S3_checkm2_ACCESS}
+    export AWS_SECRET_ACCESS_KEY=!{S3_checkm2_SECRET}
+  fi
+
+  # Download checkm database if necessary
+  mkdir -p ${DATABASE}
+  flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \
+    --link=!{DOWNLOAD_LINK} \
+    --httpsCommand="wget -O checkm2.tar.gz !{DOWNLOAD_LINK} && tar -xzvf checkm2.tar.gz && rm checkm2.tar.gz" \
+    --s3FileCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} checkm2.tar.gz && tar -xzvf checkm2.tar.gz && rm checkm2.tar.gz" \
+    --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \
+    --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \
+    --localCommand="tar -xzvf !{DOWNLOAD_LINK}" \
+    --expectedMD5SUM=!{MD5SUM}
+ 
+  export CHECKM2DB=$(find $DATABASE -name "*.dmnd")
+else
+  export CHECKM2DB=$(find !{EXTRACTED_DB} -name "*.dmnd")
+fi
+
+checkm2 predict !{params.steps.magAttributes.checkm2.additionalParams} --threads !{task.cpus} --input !{bins} -o out
+mv out/quality_report.tsv ${OUTPUT}
+
+# Prepare output
+
+# Rename column names to upper letters
+sed -i -e " 1,1 s/Name/BIN_ID/" \
+    -e " 1,1 s/Completeness/COMPLETENESS/" \
+    -e " 1,1 s/Contamination/CONTAMINATION/" ${OUTPUT}
+
+# Add missing file ending
+sed -i " 2,$ s/\t/!{ending}\t/" ${OUTPUT}
+
+# Add sample id
+sed -i -e "1s/^/SAMPLE\t/" -e "2,$ s/^/!{sample}\t/" ${OUTPUT}
+
+# Add Heterogeneity column to make it compatible with older checkm result files
+sed -i -e " 1,1 s/$/\tHETEROGENEITY/" \
+	-e " 2,$ s/$/\t0/g" ${OUTPUT}