diff --git a/.circleci/config.yml b/.circleci/config.yml
index fa4edc2d..ff30bc73 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -10,7 +10,7 @@ version: 2.1
 jobs:
   build_and_dryrun:
     <<: *defaults
-    resource_class: small
+    resource_class: medium
     environment:
       N_THREADS: 1
       MEM: 2
@@ -304,27 +304,27 @@ workflows:
   build_and_test:
     jobs:
       - build_and_dryrun
-      - genome_quantify:
-          requires:
-            - build_and_dryrun
-      - get_example_data
+      # - genome_quantify:
+      #     requires:
+      #       - build_and_dryrun
+      #- get_example_data
 
       # - run_test:
       #     requires:
       #       - build_and_dryrun
       #       - get_example_data
             
-      - qc_and_assembly:
-          requires:
-            - build_and_dryrun
-            - get_example_data
+      # - qc_and_assembly:
+      #     requires:
+      #       - build_and_dryrun
+      #       - get_example_data
 
-      - binning:
-          requires:
-            - qc_and_assembly
-      - genecatalog:
-          requires:
-            - qc_and_assembly
+      # - binning:
+      #     requires:
+      #       - qc_and_assembly
+      # - genecatalog:
+      #     requires:
+      #       - qc_and_assembly
       # - getenvs:
       #     requires:
       #       - build_and_dryrun
diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index c809b588..028c8b61 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -1,55 +1,351 @@
-name: Python Package using Conda
+name: Combined Workflow
 
-on: [push]
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+
+defaults:
+  run:
+    shell: bash -el {0} # use default shell
+
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-  build-linux:
+  build-and-dryrun:
     runs-on: ubuntu-latest
     strategy:
-      max-parallel: 5
-    defaults:
-      run:
-        shell: bash -el {0} # use default shell
+      max-parallel: 1
 
-    steps:
 
+    steps:
       - name: Checkout
         uses: actions/checkout@v3.5.2
-        
-      - name: Setup_conda_and_cache
-        uses: actions/cache@v2
-        env:
-          # Increase this value to reset cache if etc/example-environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('atlasenv.yml') }}
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          activate-environment: atlasenv
-          use-mamba: true
-          python-version: 3.11
-          mamba-version: "*"
-          channels: conda-forge,bioconda,defaults
+
+      # - name: Get current month
+      #   id: date
+      #   run: echo "date=$(date +%Y-%m)" >> "${GITHUB_OUTPUT}"
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
           environment-file: atlasenv.yml
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          environment-name: atlasenv
+          # persist on the same month.
+          cache-environment-key: atlasenv-  #${{ steps.date.outputs.date }}
 
 
       - name: Install atlas
         run: |
-           echo "You are using env '$CONDA_PREFIX'"
            python -m pip install . --no-deps -vv
+
       - name: Test atlas
         run: |
           atlas --help
           atlas --version
-      - name: Import atlas
+
+      - name: test import modules atlas
         run: |
           python -c "from atlas import utils"
 
       - name: Dryrun
+        run: test/dryrun.sh
+
+
+
+  run-qc-and-assembly:
+    runs-on: ubuntu-latest
+    needs: build-and-dryrun
+    env:
+      N_THREADS: 2
+      MEM: 0.8
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3.5.2
+
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: atlasenv.yml
+          environment-name: atlasenv
+          cache-environment-key: atlasenv-
+
+
+      - name: Install atlas
+        run: |
+          python -m pip install . --no-deps -vv
+          atlas --help
+
+      - name: get example data
+        id: get-data
+        uses: actions/cache/restore@v3
+        with:
+          path: test_reads.tar.gz
+          key: example-data
+
+      - name: Download test data
+        if: steps.get-data.outputs.cache-hit != 'true'
+        run: wget --quiet https://zenodo.org/record/3992790/files/test_reads.tar.gz
+          
+      - name: cache example data
+        if: steps.get-data.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v3
+        with:
+          path: test_reads.tar.gz
+          key: ${{ steps.get-data.outputs.cache-primary-key }}
+        
+      - name: extract data
+        run: |
+          tar -xzf test_reads.tar.gz 
+          ls -l test_reads
+
+      - name: get conda envs
+        id: get-envs
+        uses: actions/cache/restore@v3
+        with:
+          path: databases
+          key: conda-envs-assembly
+  
+        # - name: upack conda envs
+        #   if: steps.get-envs.outputs.cache-hit != 'true'
+        #   run: tar -xzf assembly_conda_envs.tar.gz
+
+
+      - name: Init
+        run: |
+          atlas init "test_reads" --threads "$N_THREADS" --working-dir wd
+
+
+      - name: Install dependencies for qc and assembly
+        if: steps.get-envs.outputs.cache-hit != 'true'
+        run: atlas run assembly --conda-create-envs-only -w wd
+
+      - name: List envs
+        run: ls -l databases/conda_envs
+
+      - name: Store conda envs
+        if: steps.get-envs.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v3
+        with:
+          path: databases
+          key: ${{ steps.get-envs.outputs.cache-primary-key }}
+
+
+      - name: Run QC
+        run: |
+          atlas run qc --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd
+
+      - name: Test Assembly
+        run: |
+          atlas run assembly --max-mem $MEM --jobs=$N_THREADS --restart-times=2 --working-dir wd
+
+      - name: Store Logs
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: wd/logs
+
+      - name: Store Sample Logs
+        uses: actions/upload-artifact@v2
+        with:
+          name: sample_logs
+          path: wd/sample1/logs
+
+      - name: Store reports
+        uses: actions/upload-artifact@v2
+        with:
+          name: reports
+          path: wd/reports
+
+
+      - name: Cache working dir
+        uses: actions/cache/save@v3
+        with:
+          path: wd
+          key: assembly-working-dir
+      
+  
+
+  run-genecatalog:
+    runs-on: ubuntu-latest
+    needs: [ build-and-dryrun, run-qc-and-assembly ]
+    env:
+      N_THREADS: 2
+      MEM: 3
+
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3.5.2
+
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: atlasenv.yml
+          environment-name: atlasenv
+          cache-environment-key: atlasenv-
+
+
+      - name: install atlas
+        run: |
+          python -m pip install . --no-deps -vv
+          atlas --help
+
+
+      - name: get conda envs
+        id: get-envs
+        uses: actions/cache/restore@v3
+        with:
+          path: databases
+          key: conda-envs-genecatalog
+          restore-keys: |
+            conda-envs-assembly
+            conda-envs-
+
+      - name: Restore working dir
+        uses: actions/cache/restore@v3
+        with:
+          path: wd
+          key: assembly-working-dir
+
+      - name: dryrun assembly shold need nothing to be done
+        run: |
+          ls -l wd
+          ls -l databases/conda_envs
+          atlas run assembly -w wd -n
+
+  
+      - name: test Genecatalog
         run: |
-          test/dryrun.sh
+          atlas run genecatalog --restart-times=2 --working-dir wd --omit-from combine_egg_nogg_annotations combine_dram_genecatalog_annotations 
+
+      - name: Store Logs
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: wd/logs
+
+      - name: Store Sample Logs
+        uses: actions/upload-artifact@v2
+        with:
+          name: sample_logs
+          path: wd/sample1/logs
+
+      - name: Store conda envs
+        #if: steps.get-envs.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v3
+        with:
+          path: databases
+          key: ${{ steps.get-envs.outputs.cache-primary-key }}
+
+
+  run-binning:
+    runs-on: ubuntu-latest
+    needs: [ build-and-dryrun, run-qc-and-assembly ]
+    env:
+      N_THREADS: 2
+      MEM: 3
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3.5.2
+
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: atlasenv.yml
+          environment-name: atlasenv
+          cache-environment-key: atlasenv-
+
+
+      - name: install atlas
+        run: |
+          python -m pip install . --no-deps -vv
+          atlas --help
+
+
+      - name: get conda envs
+        id: get-envs
+        uses: actions/cache/restore@v3
+        with:
+          path: databases
+          key: conda-envs-binning
+          restore-keys: |
+            conda-envs-
+
+      - name: Restore working dir
+        uses: actions/cache/restore@v3
+        with:
+          path: wd
+          fail-on-cache-miss: true
+          key: assembly-working-dir
+
+      - name: dryrun assembly shold need nothing to be done
+        run: |
+          ls -l wd
+          ls -l databases
+          ls -l databases/conda_envs
+          atlas run assembly -w wd -n
+
+  
+      - name: test binning
+        run: |
+          atlas run binning --restart-times=2 --working-dir wd --omit-from checkm2_download_db
+
+      - name: Store Logs
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs
+          path: wd/logs
+
+      - name: Store Sample Logs
+        uses: actions/upload-artifact@v2
+        with:
+          name: sample_logs
+          path: wd/sample1/logs
+
+      - name: Store conda envs
+       # if: steps.get-envs.outputs.cache-hit != 'true'
+        uses: actions/cache/save@v3
+        with:
+          path: databases
+          key: ${{ steps.get-envs.outputs.cache-primary-key }}
+
+  # run-quantify-genomes:
+  #   runs-on: ubuntu-latest
+  #   needs: build-and-dryrun
+
+  #   steps:
+  #     - name: Checkout
+  #       uses: actions/checkout@v3.5.2
+
+
+  #     - uses: mamba-org/setup-micromamba@v1
+  #       with:
+  #         environment-file: atlasenv.yml
+  #         environment-name: atlasenv
+  #         cache-environment-key: atlasenv-
+
+
+  #     - name: Install atlas
+  #       run: |
+  #         python -m pip install . --no-deps -vv
+  #         atlas --help
+
+
+  #     - name: get conda envs
+  #       id: get-envs
+  #       uses: actions/cache/restore@v3
+  #       with:
+  #         path: databases
+  #         key: conda-envs-assembly
+  #         restore-keys: conda-envs-*
 
diff --git a/atlas/atlas.py b/atlas/atlas.py
index 6edcfee2..7d9fef92 100644
--- a/atlas/atlas.py
+++ b/atlas/atlas.py
@@ -9,7 +9,7 @@
 
 from snakemake.io import load_configfile
 from .make_config import validate_config
-from .init.atlas_init import run_init#, run_init_sra
+from .init.atlas_init import run_init  # , run_init_sra
 
 from .__init__ import __version__
 
@@ -66,7 +66,7 @@ def cli(obj):
 cli.add_command(run_init)
 
 
-#cli.add_command(run_init_sra)
+# cli.add_command(run_init_sra)
 
 
 def get_snakefile(file="workflow/Snakefile"):
diff --git a/atlas/init/atlas_init.py b/atlas/init/atlas_init.py
index 680fea43..f8b6d062 100644
--- a/atlas/init/atlas_init.py
+++ b/atlas/init/atlas_init.py
@@ -62,7 +62,6 @@ def prepare_sample_table_for_atlas(
 
     sample_table["BinGroup"] = "All"
 
-
     validate_sample_table(sample_table)
 
     sample_table.to_csv(outfile, sep="\t")
diff --git a/atlas/make_config.py b/atlas/make_config.py
index dd8365c1..a56b5b9c 100644
--- a/atlas/make_config.py
+++ b/atlas/make_config.py
@@ -236,8 +236,6 @@ def make_config(
         )
 
 
-
-
 def validate_config(config, workflow):
     conf = load_configfile(config)
 
diff --git a/atlas/sample_table.py b/atlas/sample_table.py
index 1c127d1b..dba15a00 100644
--- a/atlas/sample_table.py
+++ b/atlas/sample_table.py
@@ -93,7 +93,7 @@ def validate_bingroup_size_cobinning(sampleTable, logger):
         logger.error(
             "If you want to use co-binning, you should have at least 5-10 samples per bin group. \n"
         )
-        BinGroupSizeError("BinGroup too small")
+        raise BinGroupSizeError("BinGroup too small")
 
 
 def validate_bingroup_size_metabat(sampleTable, logger):
diff --git a/test/dryrun.sh b/test/dryrun.sh
index f6c8d733..468f5bab 100755
--- a/test/dryrun.sh
+++ b/test/dryrun.sh
@@ -12,17 +12,37 @@ atlas run --help
 databaseDir="test/databases"
 WD='test/Dryrun'
 reads_dir='test/reads/empty'
+snakemake_args=" --quiet rules $@ --dryrun " 
+test_script_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
 
-echo "touch reads dir"
+
+create_reads_dir() {
+
+    local reads_dir="$1"
+    local N=$2
+
+echo "touch reads dir: $reads_dir"
+
+rm -rf $reads_dir
 mkdir -p $reads_dir
-for sample in Sample1 Sample2 Sample3 Sample4 Sample5 Sample6; 
-  do
+
+for (( i=1; i<=$N; i++ )); do
+    sample="Sample$i"
+    
   for fraction in R1 R2;
     do
     touch $reads_dir/${sample}_${fraction}.fastq.gz
   done
 done
+}
+
+# need at least 10 samples for cobinning
+
+create_reads_dir $reads_dir 10 
+
+
+
 
 
 rm -fr $WD
@@ -37,10 +57,10 @@ atlas init --db-dir $databaseDir --threads=$NThreads -w $WD $reads_dir
 
 
 echo "Dryrun all"
-atlas run all -w $WD --max-mem $MaxMem --jobs $NThreads --dryrun $@
+atlas run all -w $WD  $snakemake_args
 
 echo "Dryrun strains"
-atlas run genomes strains -w $WD --max-mem $MaxMem --jobs $NThreads --dryrun $@
+atlas run genomes strains -w $WD $snakemake_args
 
 
 for binner in metabat SemiBin vamb DASTool ; do
@@ -49,7 +69,7 @@ for binner in metabat SemiBin vamb DASTool ; do
         Dryrun Binner $binner
       "
 
-  atlas run genomes -w $WD --config final_binner=$binner --dryrun $@
+  atlas run binning -w $WD --config final_binner=$binner $snakemake_args
 
 done
 
@@ -60,20 +80,45 @@ echo "
       Dryrun with skip QC and megahit
     "
 #
+
+rm -fr $WD
+
 WD=${WD}/noQC
 rm -fr $WD
-atlas init --db-dir $databaseDir --threads=$NThreads --skip-qc -w $WD --assembler megahit $reads_dir
 
-atlas run all -w $WD --dryrun $@
+atlas init --db-dir $databaseDir --skip-qc -w $WD --assembler megahit $reads_dir
 
+atlas run all -w $WD $snakemake_args
 
-echo
 
 echo "
       execution with profile
     "
 
   mkdir -p $WD/local
-  printf 'cores: 1\n' > $WD/local/config.yaml
+  printf 'cores: 2\n' > $WD/local/config.yaml
+
+  atlas run qc -w $WD  --profile $WD/local $snakemake_args
+
+
+# clean up
+rm -rf $WD $reads_dir
+
+
+
+
+
+
+echo " 
+      test with external genomes
+      "
+
+bash $test_script_dir/test_external_genomes.sh $snakemake_args
+
+
+
+echo " 
+      test init with different samples
+      "
 
-  atlas run qc -w $WD --dryrun --max-mem $MaxMem --jobs $NThreads --profile $WD/local $@ 
+bash $test_script_dir/test_init_many_samples.sh $snakemake_args
\ No newline at end of file
diff --git a/test/test_ci.sh b/test/test_ci.sh
index dd9b72cf..01ced696 100755
--- a/test/test_ci.sh
+++ b/test/test_ci.sh
@@ -9,18 +9,20 @@ set -exuo pipefail
 atlas --version
 
 # get test reads
-#wget https://zenodo.org/record/3992790/files/test_reads.tar.gz
-#tar -xzf test_reads.tar.gz 
+wget https://zenodo.org/record/3992790/files/test_reads.tar.gz
+tar -xzf test_reads.tar.gz 
 
 
+ls -l test_reads
+
 databaseDir="databases"
 WD='test_ci'
-reads_dir="example_data/reads/test"
+reads_dir="test_reads" #"example_data/reads/test"
 
 
 rm -f $WD/samples.tsv
 #
-atlas init --db-dir --interleaved-fastq $databaseDir  -w $WD $reads_dir
+atlas init $reads_dir --db-dir  $databaseDir  -w $WD #--interleaved-fastq
 
 atlas run None screen -w $WD qc  $@
 
diff --git a/test/test_external_genomes.sh b/test/test_external_genomes.sh
index 1f0b123f..0d5abc06 100755
--- a/test/test_external_genomes.sh
+++ b/test/test_external_genomes.sh
@@ -12,7 +12,7 @@ MaxMem=3
 databaseDir="test/databases"
 WD='test/genome_quant'
 reads_dir='test/reads/empty'
-
+snakemake_args=" --quiet rules $@ --dryrun " 
 
 echo "touch reads dir"
 mkdir -p $reads_dir
@@ -41,4 +41,7 @@ atlas init --db-dir $databaseDir --skip-qc -w $WD $reads_dir
 
 echo "Run"
 
-atlas run None quantify_genomes -w $WD --config genome_dir="other_genomes" --dryrun $@
\ No newline at end of file
+atlas run quantify_genomes -w $WD --config genome_dir="other_genomes" $snakemake_args
+
+
+rm -rf $WD $reads_dir
\ No newline at end of file
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 3e520ff6..4e2eb047 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -40,7 +40,7 @@ wildcard_constraints:
 include: "rules/sample_table.smk"
 include: "rules/download.smk"  # contains hard coded variables
 include: "rules/qc.smk"
-include: "rules/screen.smk" # expects function get_input_fastq defined in qc
+include: "rules/screen.smk"  # expects function get_input_fastq defined in qc
 include: "rules/assemble.smk"
 include: "rules/binning.smk"
 include: "rules/derep.smk"
@@ -201,9 +201,10 @@ rule qc:
     output:
         touch("finished_QC"),
 
+
 rule screen:
     input:
-        "QC/screen/sketch_comparison.tsv.gz"
+        "QC/screen/sketch_comparison.tsv.gz",
 
 
 # overwrite commands in rules/download.snakefile
@@ -222,14 +223,12 @@ onerror:
 
 for r in workflow.rules:
     if not "mem_mb" in r.resources:
-
         if "mem" in r.resources:
             r.resources["mem_mb"] = r.resources["mem"] * 1000
         else:
             # default
             r.resources["mem_mb"] = config["mem"] * 1000
 
-
     # add time if ot present. Simple jobs use simple time
 
     if "time_min" not in r.resources:
diff --git a/workflow/rules/assemble.smk b/workflow/rules/assemble.smk
index ea88f14c..74e2e2f7 100644
--- a/workflow/rules/assemble.smk
+++ b/workflow/rules/assemble.smk
@@ -70,7 +70,6 @@ if SKIP_QC & (len(MULTIFILE_FRACTIONS) < 3):
                 -Xmx{resources.java_mem}G 2> {log}
             """
 
-
 else:
 
     localrules:
@@ -97,7 +96,6 @@ else:
 
 
 
-
 #
 rule normalize_reads:
     input:
@@ -273,7 +271,6 @@ if config.get("assembler", "megahit") == "megahit":
         shell:
             "cat {input} > {output}"
 
-
     def megahit_input_parsing(input):
         Nfiles = len(input)
 
@@ -350,7 +347,6 @@ if config.get("assembler", "megahit") == "megahit":
         shell:
             "cp {input} {output}"
 
-
 else:
     if PAIRED_END:
         ASSEMBLY_FRACTIONS = ["R1", "R2"]
@@ -465,16 +461,17 @@ else:
             temp("{sample}/assembly/{sample}_raw_contigs.fasta"),
         shell:
             "cp {input} {output}"
-# standardizes header labels within contig FASTAs
 
 
+# standardizes header labels within contig FASTAs
+
 
 rule rename_contigs:
     input:
         "{sample}/assembly/{sample}_raw_contigs.fasta",
     output:
         fasta="{sample}/assembly/{sample}_prefilter_contigs.fasta",
-        mapping_table = "{sample}/assembly/old2new_contig_names.tsv"
+        mapping_table="{sample}/assembly/old2new_contig_names.tsv",
     threads: config.get("simplejob_threads", 1)
     resources:
         mem=config["simplejob_mem"],
@@ -489,8 +486,6 @@ rule rename_contigs:
         "../scripts/rename_assembly.py"
 
 
-
-
 if config["filter_contigs"]:
 
     ruleorder: align_reads_to_prefilter_contigs > align_reads_to_final_contigs
@@ -570,9 +565,10 @@ if config["filter_contigs"]:
             minl={params.minl} \
             trim={params.trim} \
             -Xmx{resources.java_mem}G 2> {log}"""
-# HACK: this makes two copies of the same file
 
 
+# HACK: this makes two copies of the same file
+
 
 else:  # no filter
 
diff --git a/workflow/rules/binning.smk b/workflow/rules/binning.smk
index a1082726..233d2da7 100644
--- a/workflow/rules/binning.smk
+++ b/workflow/rules/binning.smk
@@ -137,11 +137,13 @@ rule get_metabat_depth_file:
         "{sample}/binning/metabat/metabat.log",
     conda:
         "../envs/metabat.yaml"
-    threads: config["threads"] # multithreaded trough OMP_NUM_THREADS
+    threads: config["threads"]  # multithreaded trough OMP_NUM_THREADS
     resources:
-        mem_mb=config["mem"]*1000,
+        mem_mb=config["mem"] * 1000,
     params:
-        minid = lambda wc, input: config["cobinning_readmapping_id"] *100 if len(input.bams)>1 else 97
+        minid=lambda wc, input: config["cobinning_readmapping_id"] * 100
+        if len(input.bams) > 1
+        else 97,
     shell:
         "jgi_summarize_bam_contig_depths "
         " --percentIdentity {params.minid} "
diff --git a/workflow/rules/cobinning.smk b/workflow/rules/cobinning.smk
index d68d7d79..810ab7e0 100644
--- a/workflow/rules/cobinning.smk
+++ b/workflow/rules/cobinning.smk
@@ -30,14 +30,14 @@ rule filter_contigs:
 
 
 def get_samples_of_bingroup(wildcards):
-
-    samples_of_group= sampleTable.query(f'BinGroup=="{wildcards.bingroup}"').index.tolist()
+    samples_of_group = sampleTable.query(
+        f'BinGroup=="{wildcards.bingroup}"'
+    ).index.tolist()
 
     return samples_of_group
 
 
 def get_filtered_contigs_of_bingroup(wildcards):
-
     samples_of_group = get_samples_of_bingroup(wildcards)
 
     if len(samples_of_group) < 5:
@@ -51,7 +51,6 @@ def get_filtered_contigs_of_bingroup(wildcards):
 
 
 def get_bams_of_bingroup(wildcards):
-
     samples_of_group = get_samples_of_bingroup(wildcards)
 
     return expand(
@@ -63,7 +62,7 @@ def get_bams_of_bingroup(wildcards):
 
 rule combine_contigs:
     input:
-        fasta= get_filtered_contigs_of_bingroup,
+        fasta=get_filtered_contigs_of_bingroup,
     output:
         "Intermediate/cobinning/{bingroup}/combined_contigs.fasta.gz",
     log:
@@ -80,9 +79,9 @@ rule combine_contigs:
                 with gz.open(input_fasta, "rb") as fin:
                     for line in fin:
                         # if line is a header add sample name
-                        if line[0] == ord('>'):
+                        if line[0] == ord(">"):
                             line = f">{sample}{params.seperator}".encode() + line[1:]
-                        # write each line to the combined file
+                            # write each line to the combined file
                         fout.write(line)
 
 
@@ -95,7 +94,7 @@ rule minimap_index:
         index_size="12G",
     resources:
         mem=config["mem"],  # limited num of fatnodes (>200g)
-    threads: config["simplejob_threads"],
+    threads: config["simplejob_threads"]
     log:
         "logs/cobinning/{bingroup}/minimap_index.log",
     benchmark:
@@ -142,7 +141,9 @@ rule minimap:
     shell:
         """minimap2 -t {threads} -ax sr {input.mmi} {input.fq} | grep -v "^@" | cat {input.dict} - | samtools view -F 3584 -b - > {output.bam} 2>{log}"""
 
-    # samtools filters out secondary alignments
+
+# samtools filters out secondary alignments
+
 
 ruleorder: sort_bam > minimap
 
@@ -156,8 +157,8 @@ rule sort_bam:
         prefix="Intermediate/cobinning/{bingroup}/bams/tmp.{sample}",
     threads: 2
     resources:
-        mem_mb=config["simplejob_mem"] *1000,
-        time_min=int(config["runtime"]["simplejob"]*60),
+        mem_mb=config["simplejob_mem"] * 1000,
+        time_min=int(config["runtime"]["simplejob"] * 60),
     log:
         "logs/cobinning/{bingroup}/mapping/sortbam/{sample}.log",
     conda:
@@ -175,14 +176,14 @@ rule summarize_bam_contig_depths:
         "logs/cobinning/{bingroup}/combine_coverage.log",
     conda:
         "../envs/metabat.yaml"
-    threads: config["threads"] # multithreaded trough OMP_NUM_THREADS
+    threads: config["threads"]  # multithreaded trough OMP_NUM_THREADS
     benchmark:
         "logs/benchmarks/cobinning/{bingroup}/summarize_bam_contig_depths.tsv"
     resources:
-        mem_mb=config["mem"]*1000,
-        time_min = config["runtime"]["long"]*60
+        mem_mb=config["mem"] * 1000,
+        time_min=config["runtime"]["long"] * 60,
     params:
-        minid = config["cobinning_readmapping_id"] *100
+        minid=config["cobinning_readmapping_id"] * 100,
     shell:
         "jgi_summarize_bam_contig_depths "
         " --percentIdentity {params.minid} "
@@ -218,8 +219,8 @@ rule run_vamb:
         "../envs/vamb.yaml"
     threads: config["threads"]
     resources:
-        mem_mb=config["mem"]*1000,
-        time_min=config["runtime"]["long"]*60,
+        mem_mb=config["mem"] * 1000,
+        time_min=config["runtime"]["long"] * 60,
     log:
         "logs/cobinning/run_vamb/{bingroup}.log",
     benchmark:
@@ -258,7 +259,7 @@ rule parse_vamb_output:
         fasta_extension=".fna",
         output_path=lambda wc: vamb_cluster_attribution_path,  # path with {sample} to replace
         samples=SAMPLES,
-        bingroups = sampleTable.BinGroup.unique()
+        bingroups=sampleTable.BinGroup.unique(),
     conda:
         "../envs/fasta.yaml"
     script:
diff --git a/workflow/rules/derep.smk b/workflow/rules/derep.smk
index 60f0f352..63312277 100644
--- a/workflow/rules/derep.smk
+++ b/workflow/rules/derep.smk
@@ -42,7 +42,6 @@ rule skani_2_parquet:
     threads: 1
     run:
         try:
-
             skani_column_dtypes = {
                 "Ref_file": "category",
                 "Query_file": "category",
diff --git a/workflow/rules/genecatalog.smk b/workflow/rules/genecatalog.smk
index 313cd485..f82e0a2a 100644
--- a/workflow/rules/genecatalog.smk
+++ b/workflow/rules/genecatalog.smk
@@ -50,7 +50,6 @@ if config["genecatalog"]["source"] == "contigs":
             cat_files(input.fna, output.fna)
             cat_files(input.short, output.short)
 
-
 else:
 
     localrules:
@@ -175,15 +174,15 @@ if (config["genecatalog"]["clustermethod"] == "linclust") or (
             "logs/Genecatalog/clustering/generate_orf_info.log",
         script:
             "../scripts/generate_orf_info.py"
-# cluster genes with cd-hit-est
 
 
+# cluster genes with cd-hit-est
+
 
 elif config["genecatalog"]["clustermethod"] == "cd-hit-est":
 
     include: "cdhit.smk"
 
-
 else:
     raise Exception(
         "Didn't understood the genecatalog clustermethod: {}".format(
@@ -388,7 +387,6 @@ rule combine_gene_coverages:
 old_subset_folder = Path("Genecatalog/subsets/genes")
 new_subset_folder = "Intermediate/genecatalog/subsets"
 if old_subset_folder.exists():
-
     logger.info(f"I move {old_subset_folder} to {new_subset_folder}")
 
     import shutil
@@ -416,7 +414,6 @@ checkpoint gene_subsets:
 
 
 def get_subset_names(wildcards):
-
     dir_for_subsets = Path(checkpoints.gene_subsets.get(**wildcards).output[0])
     subset_names = glob_wildcards(str(dir_for_subsets / "{subset}.faa")).subset
 
@@ -518,7 +515,6 @@ rule combine_egg_nogg_annotations:
         time=config["runtime"]["default"],
     run:
         try:
-
             import pandas as pd
 
             Tables = [
@@ -538,7 +534,6 @@ rule combine_egg_nogg_annotations:
 
             combined.to_parquet(output[0], index=False)
         except Exception as e:
-
             import traceback
 
             with open(log[0], "w") as logfile:
@@ -566,7 +561,6 @@ rule convert_eggNOG_tsv2parquet:
             df.to_parquet(output[0], index=False)
 
         except Exception as e:
-
             import traceback
 
             with open(log[0], "w") as logfile:
@@ -618,7 +612,6 @@ rule DRAM_annotate_genecatalog:
 
 
 def combine_genecatalog_dram_input(wildcards):
-
     all_subsets = get_subset_names(wildcards)
 
     return expand(
diff --git a/workflow/rules/genomes.smk b/workflow/rules/genomes.smk
index c17db795..ea53d19d 100644
--- a/workflow/rules/genomes.smk
+++ b/workflow/rules/genomes.smk
@@ -90,7 +90,7 @@ rule get_contig2genomes:
                 if ext == ".gz":
                     bin_name = os.path.splitext(bin_name)[0]
 
-                # write names of contigs in mapping file
+                    # write names of contigs in mapping file
                 with open(fasta) as f:
                     for line in f:
                         if line[0] == ">":
@@ -226,7 +226,6 @@ if config["genome_aligner"] == "minimap":
         wrapper:
             "v1.19.0/bio/minimap2/aligner"
 
-
 elif config["genome_aligner"] == "bwa":
 
     rule index_genomes:
@@ -262,7 +261,6 @@ elif config["genome_aligner"] == "bwa":
         wrapper:
             "v1.19.0/bio/bwa-mem2/mem"
 
-
 else:
     raise Exception(
         "'genome_aligner' not understood, it should be 'minimap' or 'bwa', got '{genome_aligner}'. check config file".format(
diff --git a/workflow/rules/qc.smk b/workflow/rules/qc.smk
index 360e0860..1629ed85 100644
--- a/workflow/rules/qc.smk
+++ b/workflow/rules/qc.smk
@@ -184,7 +184,6 @@ if not SKIP_QC:
                 " -Xmx{resources.java_mem}G "
                 " 2> {log}"
 
-
     PROCESSED_STEPS.append("filtered")
 
     rule apply_quality_filter:
@@ -209,8 +208,8 @@ if not SKIP_QC:
         params:
             ref=(
                 "ref=%s" % config.get("preprocess_adapters")
-            if config.get("preprocess_adapters")
-            else ""
+                if config.get("preprocess_adapters")
+                else ""
             ),
             mink=(
                 ""
@@ -302,7 +301,6 @@ if not SKIP_QC:
             " -Xmx{resources.java_mem}G "
             " 2> {log}"
 
-
     # if there are no references, decontamination will be skipped
     if len(config.get("contaminant_references", {}).keys()) > 0:
         PROCESSED_STEPS.append("clean")
@@ -406,7 +404,6 @@ if not SKIP_QC:
                     -Xmx{resources.java_mem}G 2>> {log}
                 """
 
-
     PROCESSED_STEPS.append("QC")
 
     localrules:
@@ -436,7 +433,7 @@ if not SKIP_QC:
                             with open(input.rrna_reads[i], "rb") as infile2:
                                 shutil.copyfileobj(infile2, outFile)
 
-            # append to sample table
+                                # append to sample table
             sample_table = load_sample_table(params.sample_table)
             qc_header = [f"Reads_QC_{fraction}" for fraction in MULTIFILE_FRACTIONS]
             sample_table.loc[wildcards.sample, qc_header] = output
@@ -444,7 +441,6 @@ if not SKIP_QC:
 
 
 
-
 #### STATS
 
 
@@ -489,7 +485,6 @@ if PAIRED_END:
             readlength.sh {params.inputs} out={output.read_length} 2>> {log}
             """
 
-
 else:
 
     rule calculate_read_length_hist:
@@ -541,7 +536,6 @@ rule combine_read_length_stats:
 
 
 
-
 # rule combine_cardinality:
 #     input:
 #         expand("{sample}/sequence_quality_control/read_stats/QC_cardinality.txt",sample=SAMPLES),
@@ -595,7 +589,6 @@ if PAIRED_END:
 
 
 
-
 localrules:
     combine_read_counts,
     write_read_counts,
diff --git a/workflow/rules/sample_table.smk b/workflow/rules/sample_table.smk
index ff0e05a3..d8155029 100644
--- a/workflow/rules/sample_table.smk
+++ b/workflow/rules/sample_table.smk
@@ -187,12 +187,11 @@ def get_assembly(wildcards):
 
     """
 
-    Header= "Assembly"
+    Header = "Assembly"
     try:
         return get_files_from_sampleTable(wildcards.sample, Header)
 
     except FileNotInSampleTableException:
         # return files as named by atlas pipeline
 
-        return "{sample}/{sample}_contigs.fasta".format(sample=wildcards.sample )
-
+        return "{sample}/{sample}_contigs.fasta".format(sample=wildcards.sample)
diff --git a/workflow/rules/screen.smk b/workflow/rules/screen.smk
index a94d185b..f60346a1 100644
--- a/workflow/rules/screen.smk
+++ b/workflow/rules/screen.smk
@@ -3,7 +3,7 @@ rule generate_sketch:
     input:
         unpack(get_input_fastq),
     output:
-        "Intermediate/screen/sketches/{sample}.sketch.gz"
+        "Intermediate/screen/sketches/{sample}.sketch.gz",
     log:
         "logs/screen/make_sketch/{sample}.log",
     conda:
@@ -14,20 +14,21 @@ rule generate_sketch:
         java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
     shell:
         "bbsketch.sh "
-        "in={input[0]}" # take only one read
+        "in={input[0]}"
         " samplerate=0.5"
         " minkeycount=2 "
         " out={output} "
         " blacklist=nt ssu=f name0={wildcards.sample} depth=t overwrite=t "
         " -Xmx{resources.java_mem}g "
         " &> {log}"
+        # take only one read
 
 
 rule compare_sketch:
     input:
-        expand( rules.generate_sketch.output, sample =SAMPLES ),
+        expand(rules.generate_sketch.output, sample=SAMPLES),
     output:
-        "QC/screen/sketch_comparison.tsv.gz"
+        "QC/screen/sketch_comparison.tsv.gz",
     priority: 100
     log:
         "logs/screen/compare_sketch.log",
@@ -46,5 +47,4 @@ rule compare_sketch:
         " &> {log}"
 
 
-
-#        sendsketch.sh sample2.sketch printdepth2=t level=2 printqfname=f printvolume=t color=f out
\ No newline at end of file
+#        sendsketch.sh sample2.sketch printdepth2=t level=2 printqfname=f printvolume=t color=f out
diff --git a/workflow/rules/semibin.smk b/workflow/rules/semibin.smk
index 761033c2..13be0cfa 100644
--- a/workflow/rules/semibin.smk
+++ b/workflow/rules/semibin.smk
@@ -73,7 +73,6 @@ rule semibin_train:
 
 
 def semibin_input(wildcards):
-
     bingroup_of_sample = sampleTable.loc[wildcards.sample, "BinGroup"]
     samples_of_bingroup = sampleTable.query(
         f'BinGroup=="{bingroup_of_sample}"'
diff --git a/workflow/scripts/combine_dram_gene_annotations.py b/workflow/scripts/combine_dram_gene_annotations.py
index 90cc3073..0dad7690 100644
--- a/workflow/scripts/combine_dram_gene_annotations.py
+++ b/workflow/scripts/combine_dram_gene_annotations.py
@@ -72,7 +72,6 @@ def handle_exception(exc_type, exc_value, exc_traceback):
         cols = db_columns[db]
 
         if not df.columns.intersection(cols).empty:
-
             Tables[db].append(df[cols].dropna(axis=0, how="all"))
 
     del df
@@ -81,7 +80,6 @@ def handle_exception(exc_type, exc_value, exc_traceback):
 out_dir.mkdir()
 
 for db in Tables:
-
     combined = pd.concat(Tables[db], axis=0)
 
     combined.sort_index(inplace=True)
diff --git a/workflow/scripts/filter_genes.py b/workflow/scripts/filter_genes.py
index fb33afc9..b399db59 100644
--- a/workflow/scripts/filter_genes.py
+++ b/workflow/scripts/filter_genes.py
@@ -34,8 +34,8 @@ def handle_exception(exc_type, exc_value, exc_traceback):
 import pyfastx
 
 
-faa_iterator = pyfastx.Fastx(snakemake.input.faa, format="fasta",comment=True)
-fna_iterator = pyfastx.Fastx(snakemake.input.fna, format="fasta",comment=True)
+faa_iterator = pyfastx.Fastx(snakemake.input.faa, format="fasta", comment=True)
+fna_iterator = pyfastx.Fastx(snakemake.input.fna, format="fasta", comment=True)
 
 
 with open(snakemake.output.faa, "w") as out_faa, open(