diff --git a/.gitignore b/.gitignore
index 626eb6b7ed3047d056a519fc0a6dcfd27c6feea8..2defeaab3edf4195e3c17e6fd3fc76fb9c9a5536 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,4 @@
-pangenome
\ No newline at end of file
+pangenome
+assembly/container/assemblySC.sif
+assembly/.snakemake
+assembly/rulegraph.pdf
\ No newline at end of file
diff --git a/README.md b/README.md
index 99fb3fc9112b551593d4d7363fd80fe76d9948ca..a1293f5307867828143b7bc0108a3607fdbd6cb8 100644
--- a/README.md
+++ b/README.md
@@ -1,8 +1,8 @@
 # Genome assembly and variant calling from PacBio HiFi reads
 
 This folder contains two Snakemake workflows:
-  - *assembly*: from PacBio HiFi consensus reads to annotated genome assemblies
-  - *variantcalling*: combine assemblies into a pangenome graph and call variants from the graph
+  - [*assembly*](assembly/README.md): from PacBio HiFi consensus reads to annotated genome assemblies
+  - [*variantcalling*](variantcalling/README.md): combine assemblies into a pangenome graph and call variants from the graph
 
 This is ongoing work, some things will change.
 
@@ -14,7 +14,7 @@ ml snakemake/6.6.1-foss-2021a
 ml Singularity/2.6.1
 ```
 
-Enter subdirectories for further information.
+<img src="fig.png"  width="50%" height="50%">
+
 
-#<img src="fig.png"  width="50%" height="50%">
 *Section of a genome graph constructed from diverse MTBC genomes. It shows a nested structural variant: an IS6110 insertion within the TBD1 region.*
diff --git a/assembly/config.yaml b/assembly/config/config.yaml
old mode 100755
new mode 100644
similarity index 89%
rename from assembly/config.yaml
rename to assembly/config/config.yaml
index ae05f92d44be64bbaa79f1ca0b62ce9ff9c77375..6b82edb7a11e09446e7191e42a029efdabee70dc
--- a/assembly/config.yaml
+++ b/assembly/config/config.yaml
@@ -2,10 +2,9 @@
 #
 ##############################
 
-samples: samples.tsv
-
 project_directory: ./results
 output_prefix: pb_bernese
+samples: config/samples.tsv
 
 ref:
   genome_size: 4.4m
diff --git a/assembly/samples.tsv b/assembly/config/samples.tsv
old mode 100755
new mode 100644
similarity index 100%
rename from assembly/samples.tsv
rename to assembly/config/samples.tsv
diff --git a/assembly/container/README.md b/assembly/container/README.md
index 9d4c1e4a3c2da5f15c022bf2b0ad04ceb36dc150..83dbaae8f9adf1e2ad0ae042dff50d18f6b29cc6 100644
--- a/assembly/container/README.md
+++ b/assembly/container/README.md
@@ -1,17 +1,4 @@
 
-Problem: 1.6 gb container on gitlab? Building or loading container requires sudo...
-
-
-```
-sudo singularity build assemblySC.sif assemblySC.def
-```
-
-
-
-
-
-
-
 # Create versioned direct file and locked dependency file (https://pythonspeed.com/articles/conda-dependency-management/)
 environment.yml: versioned main dependencies 
 conda-lock.yml: locked subdependencies
@@ -24,7 +11,6 @@ mamba install \
     samtools \
     minimap2 \
     circlator \
-    panaroo \
     prokka \
     numpy \
     scipy \
@@ -47,3 +33,9 @@ conda env update --file environment.yml --prune
 # Create locked version
 conda-lock --mamba -f environment.yml -p linux-64
 conda-lock render -p linux-64 # allows using mamba create --file conda-linux-64.lock
+
+Problem: 1.6 gb container on gitlab? Building or loading container requires sudo...
+
+```
+sudo singularity build assemblySC.sif assemblySC.def
+```
\ No newline at end of file
diff --git a/assembly/container/assemblySC.def b/assembly/container/assemblySC.def
index be3b4c236c207ba1d794520fc8bb2dccc4c279ae..51e86dedb021a39b59dabb8f53539e5e1c82df9e 100644
--- a/assembly/container/assemblySC.def
+++ b/assembly/container/assemblySC.def
@@ -8,7 +8,7 @@ From: condaforge/mambaforge:23.1.0-1
 
     export PATH=/opt/conda/bin:$PATH
 
-    mamba create --name pb_assembly --file conda-linux-64.lock
+    mamba create --name assemblySC --file conda-linux-64.lock
     mamba clean -afy
 
     apt-get clean all
@@ -22,21 +22,21 @@ From: condaforge/mambaforge:23.1.0-1
     cd LongQC/minimap2-coverage && make
 
     # Install mash
-    apt-get install -y mash
+    #apt-get install -y mash
 
     # Install polypolish
-    wget https://github.com/rrwick/Polypolish/releases/download/v0.5.0/polypolish-linux-x86_64-musl-v0.5.0.tar.gz
-    tar -xf polypolish-linux-x86_64-musl-v0.5.0.tar.gz -C /opt/conda/bin
-    rm polypolish-linux-x86_64-musl-v0.5.0.tar.gz
+    #wget https://github.com/rrwick/Polypolish/releases/download/v0.5.0/polypolish-linux-x86_64-musl-v0.5.0.tar.gz
+    #tar -xf polypolish-linux-x86_64-musl-v0.5.0.tar.gz -C /opt/conda/bin
+    #rm polypolish-linux-x86_64-musl-v0.5.0.tar.gz
 
     # Install progressiveCactus
-    wget https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.6.0/cactus-bin-v2.6.0.tar.gz
-    tar -xf cactus-bin-v2.6.0.tar.gz -C /opt/conda/bin
-    rm cactus-bin-v2.6.0.tar.gz
+    #wget https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.6.0/cactus-bin-v2.6.0.tar.gz
+    #tar -xf cactus-bin-v2.6.0.tar.gz -C /opt/conda/bin
+    #rm cactus-bin-v2.6.0.tar.gz
     
     # set to whatever your conda path is, I usually install to /opt
     echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
-    echo "conda activate pb_assembly" >> $SINGULARITY_ENVIRONMENT
+    echo "conda activate assemblySC" >> $SINGULARITY_ENVIRONMENT
 
 
 %environment
diff --git a/assembly/container/conda-linux-64.lock b/assembly/container/conda-linux-64.lock
index c09a9a3a5c489ac52771ef55751c0d15e26a2666..7a872e3ed42f97c65dec979c6a9f988eafc100f5 100644
--- a/assembly/container/conda-linux-64.lock
+++ b/assembly/container/conda-linux-64.lock
@@ -1,372 +1,279 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 182af84a8c8a1dc9eb2c6bdc76285050405b5c964d7feda7b0a4ea7d966f0976
+# input_hash: 926ab17aedcc8b15a4be8db176a2c48cafc2fcb2c9f778737a63eb301e4e346e
 @EXPLICIT
-https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda#c3473ff8bdb3d124ed5ff11ec380d6f9
-https://repo.anaconda.com/pkgs/main/linux-64/blas-1.0-mkl.conda#9a7a051e9bd41da46523acb017d8a517
-https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2023.05.30-h06a4308_0.conda#979be8dd2368decd342b13e01540d297
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://repo.anaconda.com/pkgs/main/noarch/_sysroot_linux-64_curr_repodata_hack-3-haa98f57_10.tar.bz2#3d11810264df927797876ba64fd2a714
+https://repo.anaconda.com/pkgs/main/linux-64/blas-1.0-openblas.conda#9ddfcaef10d79366c90128f5dc444be8
+https://conda.anaconda.org/bioconda/linux-64/blast-legacy-2.2.26-h9ee0642_3.tar.bz2#b7fe67ef984501e8089a142f1f58ab2f
+https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2023.08.22-h06a4308_0.conda#243d5065a09a3e85ab888c05f5b6445a
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-https://repo.anaconda.com/pkgs/main/linux-64/libgfortran4-7.5.0-ha8ba4b0_17.conda#e3883581cbf0a98672250c3e80d292bf
-https://repo.anaconda.com/pkgs/main/linux-64/openjdk-8.0.152-h7b6447c_3.conda#e3100a32e7741538a72196a721f988d9
-https://repo.anaconda.com/pkgs/main/linux-64/libgfortran-ng-7.5.0-ha8ba4b0_17.conda#ecb35c8952579d5c8dc56c6e076ba948
-https://repo.anaconda.com/pkgs/main/linux-64/libgomp-11.2.0-h1234567_1.conda#b372c0eea9b60732fdae4b817a63c8cd
-https://repo.anaconda.com/pkgs/main/linux-64/libstdcxx-ng-11.2.0-h1234567_1.conda#57623d10a70e09e1d048c2b2b6f4e2dd
-https://conda.anaconda.org/bioconda/noarch/minced-0.4.2-hdfd78af_1.tar.bz2#eee6ac504430c045623a6616e13ba833
-https://repo.anaconda.com/pkgs/main/linux-64/_openmp_mutex-5.1-1_gnu.conda#71d281e9c2192cb3fa425655a8defb85
-https://conda.anaconda.org/bioconda/linux-64/edlib-1.2.3-h2d50403_1.tar.bz2#d85cba3681b8c8b207d94f9f31737a39
-https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-11.2.0-h1234567_1.conda#a87728dabf3151fb9cfa990bd2eb0464
-https://conda.anaconda.org/bioconda/linux-64/aragorn-1.2.41-hec16e2b_0.tar.bz2#35e36bf31751b11dda35afcc2d28f89b
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2#d7c7e92a8ccc518709474dd3eda896b9
+https://repo.anaconda.com/pkgs/main/linux-64/libgfortran5-11.2.0-h1234567_1.conda#36a01a8c30e0cadf0d3e842c50b73f3b
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
+https://repo.anaconda.com/pkgs/main/noarch/tzdata-2023c-h04d1e81_0.conda#29db02adf8808f7c64642cead3e28acd
+https://repo.anaconda.com/pkgs/main/noarch/kernel-headers_linux-64-3.10.0-h57e8cba_10.tar.bz2#e3bd6db33d8c10ba1f0ec109df503827
+https://repo.anaconda.com/pkgs/main/linux-64/libgfortran-ng-11.2.0-h00389a5_1.conda#7429b67ab7b1d7cb99b9d1f3ddaec6e3
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://repo.anaconda.com/pkgs/main/noarch/sysroot_linux-64-2.17-h57e8cba_10.tar.bz2#daa11b19c141284d62536ba03f4c73aa
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
+https://conda.anaconda.org/bioconda/linux-64/aragorn-1.2.41-h031d066_1.tar.bz2#d4ed7d256f07678d839cadedd1d49443
+https://conda.anaconda.org/conda-forge/linux-64/argtable2-2.13-h14c3975_1001.tar.bz2#b9e0ac5d747ceab0c8b85a470358e1a6
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-https://conda.anaconda.org/bioconda/linux-64/clustalw-2.1-h9f5acd7_7.tar.bz2#f965c89e793fd85efcb7241d07042985
-https://repo.anaconda.com/pkgs/main/linux-64/expat-2.2.10-he6710b0_2.conda#e8b086ca590c1bd0d2a709d3affbda48
-https://repo.anaconda.com/pkgs/main/linux-64/fribidi-1.0.10-h7b6447c_0.conda#1b4851703971b3d43acdcc9c72777575
+https://repo.anaconda.com/pkgs/main/linux-64/c-ares-1.19.1-h5eee18b_0.conda#6cfbce52273a1cb888821f18ceaa83c4
+https://conda.anaconda.org/bioconda/linux-64/clustalw-2.1-h4ac6f70_9.tar.bz2#919194f6f7d733afff4d3c6f54e08d07
+https://repo.anaconda.com/pkgs/main/linux-64/expat-2.5.0-h6a678d5_0.conda#9a21d99d49a0a556cf9590430dec8ec0
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-https://repo.anaconda.com/pkgs/main/linux-64/graphite2-1.3.14-h295c915_1.conda#1939e8b3c03da6de2c021bd41aead9f9
-https://conda.anaconda.org/bioconda/linux-64/hmmer-3.3.2-h87f3376_2.tar.bz2#fefeadd4a743164946031ab491a347ab
+https://conda.anaconda.org/bioconda/linux-64/hmmer-3.3.2-hdbdd923_4.tar.bz2#805f24f8e8109e5d3d16cfad6799af46
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-https://conda.anaconda.org/bioconda/linux-64/infernal-1.1.4-h779adbc_0.tar.bz2#9f9f83d7e5e855d34af6876faf880167
 https://repo.anaconda.com/pkgs/main/linux-64/jpeg-9e-h5eee18b_1.conda#ac373800fda872108412d1ccfe3fa572
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-https://conda.anaconda.org/bioconda/linux-64/libdeflate-1.0-h14c3975_1.tar.bz2#6597b611d5070ad5fcef34a26a8065e3
-https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.2.1-hf484d3e_1007.conda#ef4c7b437f50a1ab4920dc313d8ebc28
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda#6aa9c9de5542ecb07fdda9ca626252d8
+https://repo.anaconda.com/pkgs/main/linux-64/libev-4.33-h7f8727e_1.conda#5065620db4393fb549f30114a33897d1
+https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.4.4-h6a678d5_0.conda#06e288f9250abef59b9a367d151fc339
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+https://repo.anaconda.com/pkgs/main/linux-64/libnsl-2.0.0-h5eee18b_0.conda#55e3f1b0c2a70454cdf1a5d64fb44752
+https://repo.anaconda.com/pkgs/main/linux-64/libopenblas-0.3.21-h043d6bf_0.conda#7f7324dcc3c4761a14f3e4ac443235a7
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+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/llvm-openmp-8.0.1-hc9558a2_0.tar.bz2#67590caab043d6d7ffc371f9cced7848
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-https://conda.anaconda.org/bioconda/linux-64/mafft-7.505-hec16e2b_0.tar.bz2#33da74c785690ab510469051072d5a90
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-https://conda.anaconda.org/bioconda/linux-64/paml-4.9-hec16e2b_7.tar.bz2#41888eb05cc9da15d9e2ef3bb6950f40
+https://conda.anaconda.org/bioconda/linux-64/mafft-7.520-h031d066_2.tar.bz2#5623284463f08717e04eb6cf22242301
+https://conda.anaconda.org/bioconda/linux-64/muscle-5.1-h4ac6f70_3.tar.bz2#aea487cbcbed07625e0963472c4ac568
+https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.4-h6a678d5_0.conda#5558eec6e2191741a92f832ea826251c
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.3-hd590300_0.conda#7bb88ce04c8deb9f7d763ae04a1da72f
+https://conda.anaconda.org/conda-forge/linux-64/ossuuid-1.6.2-hf484d3e_1000.tar.bz2#0ca24876ead80a9290d3936aea5fefb1
+https://conda.anaconda.org/bioconda/linux-64/paml-4.10.6-h031d066_2.tar.bz2#2adac5d4627dacbf16552a5e677a2a0b
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-https://repo.anaconda.com/pkgs/main/linux-64/perl-5.26.2-h14c3975_0.conda#146f65488ff2239f08a9f98942b60e1c
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-https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-h9a82719_1.tar.bz2#8700d84f57171e0d92bb5e7178aca95c
+https://conda.anaconda.org/bioconda/linux-64/poa-2.0-h031d066_5.tar.bz2#7f92f2dd187e08868ffc6a9e12525f75
+https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-h031d066_6.tar.bz2#05eb05a68e41b289530c1f434a63fc73
+https://repo.anaconda.com/pkgs/main/linux-64/xz-5.4.2-h5eee18b_0.conda#bcd31de48a0dcb44bc5b99675800c5cc
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+https://conda.anaconda.org/bioconda/noarch/perl-http-cookies-6.10-pl5321hdfd78af_0.tar.bz2#e814a81fb8024d2be457805250df690c
+https://conda.anaconda.org/bioconda/noarch/perl-http-daemon-6.16-pl5321hdfd78af_0.tar.bz2#55e2a97aa9794010e0f1cedc1abb3f19
+https://conda.anaconda.org/bioconda/noarch/perl-http-negotiate-6.01-pl5321hdfd78af_4.tar.bz2#8a56e406990d3b84b89a50caf5f2811d
+https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0207-pl5321h661654b_0.tar.bz2#1ce8ba66c656dbe547110201b1456797
+https://repo.anaconda.com/pkgs/main/linux-64/pyqt-5.15.7-py310h6a678d5_1.conda#2084350b18db696c9bfa61401c3c62a6
+https://repo.anaconda.com/pkgs/main/linux-64/matplotlib-3.7.2-py310h06a4308_0.conda#d82ab76c17c1328f1966a198e72ee5e7
+https://conda.anaconda.org/bioconda/linux-64/ncbi-vdb-3.0.8-hdbdd923_0.tar.bz2#3b58cf2b702f96d812c67466456fe251
+https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.67-pl5321hdfd78af_0.tar.bz2#9493077e9e1dae0017f0d4cd9baf7de6
+https://conda.anaconda.org/bioconda/linux-64/blast-2.14.1-pl5321h6f7f691_0.tar.bz2#717b2ae9b971e769e00b984e37fe8947
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+https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-xpath-0.14-pl5321hdfd78af_2.tar.bz2#b959a7e6e307abaec3f06b0bc007809a
+https://conda.anaconda.org/bioconda/linux-64/t-coffee-12.00.7fb08c2-h26a2512_0.tar.bz2#a0e9a4fa83c8c2cb485f248cf5ec0a34
+https://conda.anaconda.org/bioconda/noarch/perl-bio-featureio-1.6.905-pl5321hdfd78af_4.tar.bz2#1b4b260b45e9cac33fcb45918cda428b
+https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5321hdfd78af_5.tar.bz2#932416c9ba6a9af43609e04ec5952574
+https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.8-hdfd78af_1.tar.bz2#a693939710e572d0f85f6058b534e319
+https://conda.anaconda.org/bioconda/noarch/prokka-1.14.6-pl5321hdfd78af_5.tar.bz2#6aea788d2ca74ab50d6816e7e0a75da2
diff --git a/assembly/container/conda-lock.yml b/assembly/container/conda-lock.yml
new file mode 100644
index 0000000000000000000000000000000000000000..e2ae3a4a09caf5d45788f6fd81d8c0840bd2b5c9
--- /dev/null
+++ b/assembly/container/conda-lock.yml
@@ -0,0 +1,3959 @@
+# This lock file was generated by conda-lock (https://github.com/conda-incubator/conda-lock). DO NOT EDIT!
+#
+# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike
+# e.g. `conda env create`, the resulting environment will not change as new package versions become
+# available, unless you explicitly update the lock file.
+#
+# Install this environment as "YOURENV" with:
+#     conda-lock install -n YOURENV --file conda-lock.yml
+# To update a single package to the latest version compatible with the version constraints in the source:
+#     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
+# To re-solve the entire environment, e.g. after changing a version constraint in the source file:
+#     conda-lock -f /home/cristobal/TB/projects/pacbio_microscale/gitlab/PacbioSnake/assembly/container/environment.yml --lockfile conda-lock.yml
+metadata:
+  channels:
+  - url: defaults
+    used_env_vars: []
+  - url: conda-forge
+    used_env_vars: []
+  - url: bioconda
+    used_env_vars: []
+  - url: r
+    used_env_vars: []
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+  platforms:
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+  sources:
+  - /home/cristobal/TB/projects/pacbio_microscale/gitlab/PacbioSnake/assembly/container/environment.yml
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+  manager: conda
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+  manager: conda
+  name: _sysroot_linux-64_curr_repodata_hack
+  optional: false
+  platform: linux-64
+  url: https://repo.anaconda.com/pkgs/main/noarch/_sysroot_linux-64_curr_repodata_hack-3-haa98f57_10.tar.bz2
+  version: '3'
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+  url: https://repo.anaconda.com/pkgs/main/linux-64/blas-1.0-openblas.conda
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+  manager: conda
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+  url: https://conda.anaconda.org/bioconda/linux-64/blast-legacy-2.2.26-h9ee0642_3.tar.bz2
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+  manager: conda
+  name: ca-certificates
+  optional: false
+  platform: linux-64
+  url: https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2023.08.22-h06a4308_0.conda
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+    perl-lwp-mediatypes: ''
+    perl-mime-base64: ''
+    perl-net-http: '>=6.18'
+    perl-ntlm: ''
+    perl-try-tiny: ''
+    perl-uri: ''
+    perl-www-robotrules: ''
+  hash:
+    md5: 9493077e9e1dae0017f0d4cd9baf7de6
+    sha256: cb997a7d5ff37db0dafbcf7650645e64d23bfe0f1109c34f54e064f3bfe76a2c
+  manager: conda
+  name: perl-libwww-perl
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.67-pl5321hdfd78af_0.tar.bz2
+  version: '6.67'
+- category: main
+  dependencies:
+    bzip2: '>=1.0.8,<2.0a0'
+    curl: ''
+    entrez-direct: ''
+    libgcc-ng: '>=12'
+    libstdcxx-ng: '>=12'
+    libzlib: '>=1.2.13,<1.3.0a0'
+    ncbi-vdb: ''
+    pcre: '>=8.45,<9.0a0'
+    perl: ''
+    perl-archive-tar: ''
+    perl-json: ''
+    perl-list-moreutils: ''
+    zlib: ''
+  hash:
+    md5: 717b2ae9b971e769e00b984e37fe8947
+    sha256: a83d7e119a32a39d9d839c691d811dcea091e06dd4eac3032ab3244be606baa6
+  manager: conda
+  name: blast
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/linux-64/blast-2.14.1-pl5321h6f7f691_0.tar.bz2
+  version: 2.14.1
+- category: main
+  dependencies:
+    perl: '>=5.32.1,<6.0a0 *_perl5'
+    perl-http-message: '>=6.18'
+    perl-libwww-perl: ''
+    perl-libxml-perl: ''
+    perl-xml-parser: ''
+    perl-xml-regexp: ''
+  hash:
+    md5: 45b7ce435727456727f45b3e2121b23b
+    sha256: 5d51356aa3d2f46ff6bf060567bbaa30b4a9dcbab8d5abf9cbaa50c8a10aa369
+  manager: conda
+  name: perl-xml-dom
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-1.46-pl5321hdfd78af_1.tar.bz2
+  version: '1.46'
+- category: main
+  dependencies:
+    perl: '>=5.32.1,<6.0a0 *_perl5'
+    perl-xml-dom: ''
+    perl-xml-xpathengine: ''
+  hash:
+    md5: b959a7e6e307abaec3f06b0bc007809a
+    sha256: d50d8bf14f9562cefe230f2333b26475ffac6b859d72bae19afb02ca52a0245b
+  manager: conda
+  name: perl-xml-dom-xpath
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-xpath-0.14-pl5321hdfd78af_2.tar.bz2
+  version: '0.14'
+- category: main
+  dependencies:
+    blast: ''
+    clustalo: ''
+    clustalw: ''
+    libgcc-ng: '>=4.9'
+    libgfortran: '>=3.0'
+    libstdcxx-ng: '>=4.9'
+    mafft: ''
+    muscle: ''
+    poa: ''
+    viennarna: ''
+  hash:
+    md5: a0e9a4fa83c8c2cb485f248cf5ec0a34
+    sha256: 33055cffed0ad42ee41306759f9b10c8e0a80f44850b7a7b8a67c4e034ef2839
+  manager: conda
+  name: t-coffee
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/linux-64/t-coffee-12.00.7fb08c2-h26a2512_0.tar.bz2
+  version: 12.00.7fb08c2
+- category: main
+  dependencies:
+    perl: '>=5.32.1,<6.0a0 *_perl5'
+    perl-bioperl-core: ''
+    perl-tree-dag_node: ''
+    perl-uri: ''
+    perl-xml-dom: ''
+    perl-xml-dom-xpath: ''
+  hash:
+    md5: 1b4b260b45e9cac33fcb45918cda428b
+    sha256: d63661b5a81ddc9c80dba2992fa9391e2ca9e4da15c201113dee83becbc6a4ef
+  manager: conda
+  name: perl-bio-featureio
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/noarch/perl-bio-featureio-1.6.905-pl5321hdfd78af_4.tar.bz2
+  version: 1.6.905
+- category: main
+  dependencies:
+    perl: '>=5.32.1,<6.0a0 *_perl5'
+    perl-bioperl-run: ''
+    t-coffee: ''
+  hash:
+    md5: 932416c9ba6a9af43609e04ec5952574
+    sha256: 0ffaced1dbe89e5bd626e2d467822848b66e084d4b3fa6a21ba9af26a7133aaa
+  manager: conda
+  name: perl-bio-tools-run-alignment-tcoffee
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5321hdfd78af_5.tar.bz2
+  version: 1.7.4
+- category: main
+  dependencies:
+    perl: ''
+    perl-bio-asn1-entrezgene: ''
+    perl-bio-coordinate: ''
+    perl-bio-featureio: ''
+    perl-bio-samtools: ''
+    perl-bio-searchio-hmmer: ''
+    perl-bio-tools-phylo-paml: ''
+    perl-bio-tools-run-alignment-clustalw: ''
+    perl-bio-tools-run-alignment-tcoffee: ''
+    perl-bioperl-core: 1.7.8.*
+    perl-bioperl-run: ''
+  hash:
+    md5: a693939710e572d0f85f6058b534e319
+    sha256: 9632f59b230f0b5c9ba168ec742ba4dabc77b2cdac63ac71aaa8846f26bd4cb7
+  manager: conda
+  name: perl-bioperl
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.8-hdfd78af_1.tar.bz2
+  version: 1.7.8
+- category: main
+  dependencies:
+    aragorn: '>=1.2'
+    barrnap: '>=0.7'
+    blast: '>=2.7.1'
+    hmmer: '>=3.1b2'
+    infernal: '>=1.1.2'
+    minced: '>=0.3'
+    parallel: '>=20180522'
+    perl: '>=5.32.1,<6.0a0 *_perl5'
+    perl-bioperl: '>=1.7.2'
+    perl-xml-simple: ''
+    prodigal: '>=2.6'
+    tbl2asn-forever: '>=25.7'
+  hash:
+    md5: 6aea788d2ca74ab50d6816e7e0a75da2
+    sha256: 654e7ab399907d0153052dc2f729d4b8db5de6c819686d2dbb8a4890782595c4
+  manager: conda
+  name: prokka
+  optional: false
+  platform: linux-64
+  url: https://conda.anaconda.org/bioconda/noarch/prokka-1.14.6-pl5321hdfd78af_5.tar.bz2
+  version: 1.14.6
+version: 1
diff --git a/assembly/container/environment.yml b/assembly/container/environment.yml
index b9973f8b4e9ab3e52ee37a0a715a4d7ed4a2d2c4..cbebc99fe5b6188e4ad1fa532b91819b10d15387 100644
--- a/assembly/container/environment.yml
+++ b/assembly/container/environment.yml
@@ -1,8 +1,9 @@
-name: pb_assembly
+name: assemblySC
 channels:
+  - defaults
+  - conda-forge
   - bioconda
   - r
-  - defaults
 dependencies:
   - flye
   - samtools
@@ -20,4 +21,7 @@ dependencies:
   - edlib
   - python-edlib
   - biopython
-prefix: /home/cristobal/anaconda3/envs/pb_assembly
+  - ca-certificates
+  - certifi
+  - openssl
+prefix: /home/cristobal/anaconda3/envs/assemblySC
diff --git a/assembly/resources/H37Rv.gbf b/assembly/resources/H37Rv.gbf
old mode 100755
new mode 100644
diff --git a/assembly/workflow/rules/annotate.smk b/assembly/workflow/rules/annotate.smk
old mode 100755
new mode 100644
diff --git a/assembly/workflow/rules/assemble.smk b/assembly/workflow/rules/assemble.smk
old mode 100755
new mode 100644
diff --git a/assembly/workflow/rules/circularize.smk b/assembly/workflow/rules/circularize.smk
old mode 100755
new mode 100644
index 17a10f1e83e31d8a83b2da85e7efff29c45939d7..cce5cb3c333e117c913a5b61431727c5f7f1cea7
--- a/assembly/workflow/rules/circularize.smk
+++ b/assembly/workflow/rules/circularize.smk
@@ -1,5 +1,5 @@
 
-rule mapreads:
+rule circlator_mapreads:
     input: 
         assembly = 'results/{sample}/assembly.fasta',
         reads = lambda wildcards: expand(samples[wildcards.sample].longread_fastq)
@@ -13,7 +13,7 @@ rule mapreads:
 
         """
 
-rule bam2reads:
+rule circlator_bam2reads:
     input: "results/{sample}/circlator/01.mapreads.bam"
     output: "results/{sample}/circlator/02.bam2reads.fasta"
     params:
@@ -24,7 +24,7 @@ rule bam2reads:
 
         """
 
-rule localassembly:
+rule circlator_localassembly:
     input: "results/{sample}/circlator/02.bam2reads.fasta"
     output: "results/{sample}/circlator/03.assemble/assembly.fasta"
     params:
@@ -36,7 +36,7 @@ rule localassembly:
 
         """
 
-rule merge:
+rule circlator_merge:
     input: 
         assembly = 'results/{sample}/assembly.fasta',
         localassembly = "results/{sample}/circlator/03.assemble/assembly.fasta"
@@ -50,7 +50,7 @@ rule merge:
 
         """
 
-rule clean:
+rule circlator_clean:
     input: "results/{sample}/circlator/04.merge.fasta"
     output: "results/{sample}/circlator/05.clean.fasta"
     params:
@@ -61,7 +61,7 @@ rule clean:
 
         """
 
-rule fixstart:
+rule circlator_fixstart:
     input: "results/{sample}/circlator/05.clean.fasta"
     output: "results/{sample}/circlator/06.fixstart.fasta"
     params:
diff --git a/assembly/workflow/rules/common.smk b/assembly/workflow/rules/common.smk
old mode 100755
new mode 100644
index 63ccf25c8dfd65753d8a4c11ce0599dab46f8d80..eac2fbc0f20255a5105cdacfd40dd26496a3afe4
--- a/assembly/workflow/rules/common.smk
+++ b/assembly/workflow/rules/common.smk
@@ -1,4 +1,4 @@
-configfile: "config.yaml"
+configfile: "config/config.yaml"
 
 class sample:
     def __init__(self, fields):
diff --git a/assembly/workflow/rules/readQC.smk b/assembly/workflow/rules/readQC.smk
old mode 100755
new mode 100644
diff --git a/variantcalling/README.md b/variantcalling/README.md
index a3424f8d6b1849c468068feb1a5f254c39bb5316..ce3013ac0eb8affd8714990f28e98e3a9a2f3344 100644
--- a/variantcalling/README.md
+++ b/variantcalling/README.md
@@ -3,23 +3,18 @@
 ## assemblies.txt
 
 
-
-
-## config.yaml
+## config/config.yaml
 ```yaml
 
-samples: samples.inhouse.hifi.test.csv
-
-results_directory: ./results
-output_prefix: pb_bernese
-
-ref:
-  genome_size: 4.4m
-  gbf: resources/H37Rv.gbf
+reference: 
 
 threads: 4
 
-keep_intermediate: "Yes"
+output_dir: ./results
+
+pggb:
+  p: 99
+  s: 5k
 
 ```
 
diff --git a/variantcalling/config/biopython.yaml b/variantcalling/config/biopython.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..9b7042f57eb6b06206ba966c3ab73e3d590400aa
--- /dev/null
+++ b/variantcalling/config/biopython.yaml
@@ -0,0 +1,40 @@
+name: biopython
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+  - r
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - biopython=1.78=py311h5eee18b_0
+  - blas=1.0=mkl
+  - bzip2=1.0.8=h7b6447c_0
+  - ca-certificates=2023.08.22=h06a4308_0
+  - intel-openmp=2023.1.0=hdb19cb5_46305
+  - ld_impl_linux-64=2.38=h1181459_1
+  - libffi=3.4.4=h6a678d5_0
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libuuid=1.41.5=h5eee18b_0
+  - mkl=2023.1.0=h213fc3f_46343
+  - mkl-service=2.4.0=py311h5eee18b_1
+  - mkl_fft=1.3.8=py311h5eee18b_0
+  - mkl_random=1.2.4=py311hdb19cb5_0
+  - ncurses=6.4=h6a678d5_0
+  - numpy=1.26.0=py311h08b1b3b_0
+  - numpy-base=1.26.0=py311hf175353_0
+  - openssl=3.0.11=h7f8727e_2
+  - pip=23.2.1=py311h06a4308_0
+  - python=3.11.5=h955ad1f_0
+  - readline=8.2=h5eee18b_0
+  - setuptools=68.0.0=py311h06a4308_0
+  - sqlite=3.41.2=h5eee18b_0
+  - tbb=2021.8.0=hdb19cb5_0
+  - tk=8.6.12=h1ccaba5_0
+  - tzdata=2023c=h04d1e81_0
+  - wheel=0.41.2=py311h06a4308_0
+  - xz=5.4.2=h5eee18b_0
+  - zlib=1.2.13=h5eee18b_0
+prefix: /home/cristobal/anaconda3/envs/biopython
diff --git a/variantcalling/config.yaml b/variantcalling/config/config.yaml
similarity index 100%
rename from variantcalling/config.yaml
rename to variantcalling/config/config.yaml
diff --git a/variantcalling/samples.txt b/variantcalling/config/samples.txt
similarity index 100%
rename from variantcalling/samples.txt
rename to variantcalling/config/samples.txt
diff --git a/variantcalling/workflow/Snakefile b/variantcalling/workflow/Snakefile
index ff09382699d3de1a26f0a2651659a12ea91d304c..cc39245ce400f64986af595a1ab0d4464165df94 100644
--- a/variantcalling/workflow/Snakefile
+++ b/variantcalling/workflow/Snakefile
@@ -31,32 +31,13 @@ rule combine_assemblies:
     output: 
         fasta = "results/single_contig_assemblies.fasta",
         discarded = "results/discarded_assemblies.txt"
-    conda: "env.yaml"
+    conda: "config/biopython.yaml"
     shell:
         """
-        python ./combine_assemblies.py {input}
+        python workflow/scripts/combine_assemblies.py {input}
 
         """
-    run:
-        import sys
-        from Bio import SeqIO
-
-        fasta_handle = open(output.fasta, "w")
-        discarded = open(output.discarded, "w")
-
-        for ASSEMBLY in input:
-                            
-            records = SeqIO.parse(ASSEMBLY, "fasta")
-            if len(records) > 1:
-                discarded.write(ASSEMBLY + '\n')
-
-            else:
-                rec = next(records)
-                SeqIO.write(rec, fasta_handle, "fasta")
-
-        fasta_handle.close()
-        discarded.close()  
-
+    
 
 rule pggb:
     input: "results/single_contig_assemblies.fasta"
diff --git a/variantcalling/workflow/scripts/combine_assemblies.py b/variantcalling/workflow/scripts/combine_assemblies.py
new file mode 100644
index 0000000000000000000000000000000000000000..39321570a9e9d355b9e249789fc125b40a2c4a34
--- /dev/null
+++ b/variantcalling/workflow/scripts/combine_assemblies.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import re
+import sys
+from Bio import SeqIO
+
+
+assemblies = sys.argv[1:]
+
+fasta_handle = open("results_sim/single_contig_assemblies.fasta", "w")
+discarded = open("results_sim/discarded_assemblies.txt", "w")
+
+for ASSEMBLY in assemblies:
+                    
+    records = [rec for rec in SeqIO.parse(ASSEMBLY, "fasta")]
+    if len(records) > 1:
+        discarded.write(ASSEMBLY + '\n')
+
+    else:
+        rec = records[0]
+        SeqIO.write(rec, fasta_handle, "fasta")
+
+fasta_handle.close()
+discarded.close() 
\ No newline at end of file