Dev

.gitignore

@@ -11,6 +11,7 @@
 /vcs.xml
 /webServers.xml
 /workspace.xml
+/assets/tostadas.code-workspace
 
 # Editor-based HTTP Client requests
 /httpRequests/
@@ -22,41 +23,19 @@
 
 # nextflow
 /.nextflow/
-/.nextflow
-/.nextflow.log
-/.nextflow.log.1
-/.nextflow.log.2
-/.nextflow.log.3
-/.nextflow.log.4
-/.nextflow.log.5
-/.nextflow.log.6
-/.nextflow.log.7
-/.nextflow.log.8
+/.nextflow.log*
 /nf_test_results
 /tests/work
+/var_work/
+/var_work
+app/environment.yml
 /tests/.nextflow
 /tests/.nextflow
-/tests/.nextflow.log
-/tests/.nextflow.log.1
-/tests/.nextflow.log.2
-/tests/.nextflow.log.3
-/tests/.nextflow.log.4
-/tests/.nextflow.log.5
-/tests/.nextflow.log.6
-/tests/.nextflow.log.7
-/tests/.nextflow.log.8
+/tests/.nextflow.log*
 /submission_scripts/upload_log.csv
 
 /bin/.nextflow
-/bin/.nextflow.log
-/bin/.nextflow.log.1
-/bin/.nextflow.log.2
-/bin/.nextflow.log.3
-/bin/.nextflow.log.4
-/bin/.nextflow.log.5
-/bin/.nextflow.log.6
-/bin/.nextflow.log.7
-/bin/.nextflow.log.8
+/bin/.nextflow.log*
 /bin/upload_log.csv
 
 /submission_scripts/__pycache__/
@@ -77,6 +56,12 @@ tests/__pycache__
 /bin/vadr_outputs
 /bin/vadr_outputs/
 
+# bakta related
+# /assets
+/assets/bakta_database
+/assets/bakta_database/db_light
+/assets/bakta_database/db_light/
+
 # add singularity related stuff
 /app/singularity/containers/
 
@@ -91,18 +76,7 @@ tests/__pycache__
 /submission_scripts/config_files
 
 # add aspen related stuff
-/aspen/.nextflow.log.1
-/aspen/.nextflow.log.2
-/aspen/.nextflow.log.3
-/aspen/.nextflow.log.4
-/aspen/.nextflow.log.5
-/aspen/.nextflow.log.6
-/aspen/.nextflow.log.7
-/aspen/.nextflow.log.8
-/aspen/.nextflow.log.9
-/aspen/.nextflow.log.10
-/aspen/.nextflow.log.11
-/aspen/.nextflow.log.12
+/aspen/.nextflow.log*
 
 /tests/nf_test_results
 
@@ -127,4 +101,5 @@ bin/.DS_Store
 /test_submission
 
 # Testing related
-/test_main_workflow
+/test_main_workflow
+/validation_outputs/

app/singularity/singularity_docker_boot.def

@@ -6,15 +6,20 @@ From: continuumio/miniconda3
 
 %post
     # install mamba and create .yml file
-    /opt/conda/bin/conda install -c conda-forge mamba
-    /opt/conda/bin/mamba env create -f environment.yml
+    wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh
+    bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge
+    export PATH="$HOME/mambaforge/bin:$PATH"
+    # source $HOME/mambaforge/etc/profile.d/conda.sh
+    # conda activate
+    mamba env create -f environment.yml
 
     # change the singularity environment variable to the conda env (start env by default)
-    echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
-    echo "conda activate tostadas" >> $SINGULARITY_ENVIRONMENT
+    # echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
+    # echo "conda activate tostadas" >> $SINGULARITY_ENVIRONMENT
 
     # check if it worked
-    . /opt/conda/etc/profile.d/conda.sh
+    . $HOME/mambaforge/etc/profile.d/conda.sh
+    conda activate
     conda activate tostadas
     printf "\n\n******** LIST OF PACKAGES IN TOSTADAS ENV ********\n\n"
     conda list

assets/custom_meta_fields/example_custom_fields.json

@@ -0,0 +1,20 @@
+{
+    "test_field_1": {
+        "type": "String ",
+        "samples": ["Fl0004", "IL0005", "FL0015", "FL00234", 8],
+        "replace_empty_with": "not populated",
+        "new_field_name": "new_field_name"
+    },
+    "test_field_2": {
+        "type": "float",
+        "samples": ["Fl0004"],
+        "replace_empty_with": "",
+        "new_field_name": "new_field_name2"
+    },
+    "test_field_3": {
+        "type": "Boolean",
+        "samples": ["All ", "any random sample name"],
+        "replace_empty_with": "",
+        "new_field_name": ""
+    }
+}

assets/feature_types.txt

@@ -0,0 +1 @@
+misc_feature

assets/lib/MPOX_repeats_lib.fasta

@@ -0,0 +1,4 @@
+>MPOX_ITR1#UNKOWN
+GATAGATCGAAAAAAGCCACTAATAAAAACAGTTGGTTAATTACTTCAGGCTTTAGACTACAAAAATGGTTCGATAGCGAAGATTGTATAATTTATCTCAGATCTTTAGTTAGAAGAATGGAAGACAGTAACAAAAACAGTAAAAAAACTTAGTACTTAGATATCGAAAAAATATATTTTTGTAGACTCTTGAGAATAGAAGGAAAACATGTACATAATTATAAAAAATGAAAATCAATGGCGAATAAGACAGTGCGATTCGCACCATGGAGTCGGTAGATTTCATGGCTGTCGATGAGCAGTTTCACGACGACCTCGATCTTTGGTCATTATCTTTGGTAGATGATTATAAAAAACATGGATTAGGTGTTGACTGTTATGTTCTAGAACCAGTTGTTGACAGGAAAATATTTGATAGATTTCTCCTTGAACCAATTTGTGATCCTGTAGATGTTCTGTATGATTATTTTAGGATTCATAGAGATAATATTGATCAGTATATAGTAGATAGACTGTTTGCATATATTACATATAAAGATATTATATCTGCATTAGTGTCAAAGAATTATATGGAAGATATTTTCTCTATAATTATTAAGAATTGTAATTCTGTGCAAGATCTCTTACTTTACTATCTATCTAATGCATATGTAGAAATAGACATTGTTGATCTTATGGTAGATCATGGGGCTGTAATATATAAAATAGAATGCTTGAATGCCTATTTTAGGGGAATATGTAAAAAGGAAAGTAGTGTTGTTGAGTTTATTTTGAATTGTGGTATCCCAGATGAAAATGATGTTAAATTAGATCTATATAAAATAATTCAGTATACTAGGGGATTCCTTGTAGATGAACCCACAGTATTAGAAATTTATAAGCTTTGTATCCCATATATTGAAGATATCAATCAACTAGATGCTGGTGGAAGGACCTTGCTTTATCGCGCTATCTATGCAGGTTATATAGATTTAGTATCATGGCTATTAGAAAATGGAGCAAATGTCAACGCAGTAATGAGTAATGGATATACATGTCTTGACGTGGCCGTGGATAGGGGATCTGTCATCGCCCGTAGGGAAGCACATCTTAAAATATTAGAAATATTGCTTAGAGAACCATTGTCTATTGACTGTATAAAATTAGCTATACTTAATAATACAATTGAAAACCATGATGTGATAAAGCTCTGTATCAAGTATTTTATGATGGTAGATTATTCACTTTGTAATGTGTATGCATCATCACTCTTTGATTATATAATTGATTGTAAACAAGAATTGGAGTACATTAGGCAGATGAAAATTCATAATACAACCATGTATGAGTTAATCTATAATAGAGACAAAAACAAGCATGCTTCCCATATTCTACATAGGTATTCTAAACATCCAGTTTTGACACAGTGTATCACTAAAGGATTCAAGATTTACACAGAAGTAACCGAGCAGGTCACTAAAGCTCTAAACAGACGTGCTCTAATAGATGAGATAATAAACAATGTATCAACTGATGACAATCTCCTATCAAAACTTCCATTAGAAATTAGGGATCTAATTGTTTCACAAGCTGTCATATAGAGTTCTATCCACCCACCTTTCTTGAAATGAGTTAATAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTTATAGTCTAACACTTCTAATTTTTATACCTTGATCTTTTTCTCTAATTATGAAAAAGTAAATCATTATGAAGATGGATGAAATGGACGAGATTGTGCGCATCGTTAACGATAGTATGTGGTACGTACCTAACGCATTTATGGACGACGGTGATAATGAAGGTCACATTTCTGTCAATAATGTCTGTCATATGTATCTCGCATTCTTTGATGTGGATATATCATCTCATCTGTTTAAATTAGTTATTAAACACTGCGATCTGAATAAACGACTAAAATGTGGTAACTCTCCATTACATTGCTATACGATGAATACACGATTTAATCCATCTGTATTAAAGATATTGTTACGCCACGGCATGCGTAACTTTGATAGCAAGGATAAAAAAGGACATATTCCTCTACACCACTATCTGATTCATTCACTATCAATCGATAACAAGATCTTTGATATACTAACGGACCCCATTGATGACTTTAGTAAATCATCCGATCTATTGCTGTGTTATCTTAGATATAAATTCAATGGGAGCTTAAACTATTACGTTCTGTACAAATTATTGACTAAAGGATCTGACCCTAATTGCGTCGATGAGGATGGACTCACTTCTCTTCATTACTACTGTAAACACATATCCGCGTTCCACGAAAGCAATTATTACAAGTCAAAGAGTCACACTAAGATGCGAGCTGAGAAGCGATTCATCTACGCGATAATAGATCATGGAGCAAACATTAACGCGGTTACGAAAATCGGAAATACGCCGTTACACACTTACCTTCAACAGTATACCAAACATAGTCCTCGTGTGGTGTATGCTCTTTTATCTCGAGGAGCCGATACGAGGATACGTAATAATCTTGATTGTACACCCATCATGGAATACATAAAGAACGATTGTGCAACAGGTCATATTCTCATAATGTTACTCAATTGGCACGAACAAAAATACGGGAAATTACAAAAGGAAGAAGGACAACATCTACTTTATCTATTCATAAAACATAATCAAGGATATGGAAGTCGCTCTCTCAATATACTACGGTATCTACTAGATAGATTCGACATTCAGAAAGACGAATACTATAATACAATGACTCCTCTTCATACCGCCTTCCAGAATTGCAATAACAATGTTGCCTCATACCTCGTATACATCGGATACGACATCAACCTTCCGACTAAAGACGATAAGACAGTATTCGACTTGGTGTTTGAAAACAGAAACATTATATACAAGGCGGATGTCGTTAATGACATTATCCACCACAGACTGAAAGTATCTCTACCTATGATTAAATCGTTGTTCTACAAGATGTCGGAGTTCTCTCCCTACGACGATCACTACGTAAAGAAGATAATAGCCTACTGCCTATTAAGGGACGAGTCATTTGCGGAACTACATACTAAATTCTGTTTAAACGAGGACTATAAAAGTGTATTTATGAAAAATATATCATTCGATAAGATAGATTCCATCATCGAAAAATGTAGTCGTGACATAAGTCTCCTCAAAGAGATTCGAATCTCAGACACCGACTTGTATACGGTATTGAGAACAGAAGACATCCGGTATCACACATATCTCGAAGCCATACATTCAGACAAACGCATTTCATTTCCCATGTACGACGATCTCATAGAACAGTGTCATCTATCGATGGAGCATAAAAGTAAACTCGTCGACAAAGCACTCAATAAATTAGAGTCTACCATCGATAGTCAATCTAGACTATCGTATTTGCCTCCGGAAATTATGCGCAATATCATAACCAAGCTAAGCGACTACCATCTAAACAGTATGTTGTACGGAAAGAACCATTACAAATATTATCCATGATAGAAAGAAAATATTTAAAAAATAATCTATATGATTGGAGAAGTAGGAAACAAACAGTAACAAGACGACGATTACTACATTATTAAATCATGAGGTCCGTATTATACTCGTATATATTGTTTCTCTCATGTATAATAATAAACGGAAGAGATATAGCACCACATGCACCATCCAATGGAAAGTGTAAAGACAACGAATACAGAAGCCGTAATCTATGTTGTCTATCGTGTCCTCCGGGAACTTACGCTTCCAGATTATGTGATAGCAAGACTAATACACAATGTACACCGTGTGGTTCGGATACCTTTACATCTCACAATAATCATTTACAGGCTTGTCTAAGTTGTAACGGAAGATGTGATAGTAATCAGGTAGAGACGCGATCGTGTAACACGACTCACAATAGAATCTGTGAATGCTCTCCAGGATATTATTGTCTTCTCAAAGGAGCATCAGGGTGTAGAACATGTATTTCTAAAACAAAGTGTGGAATAGGATACGGAGTATCCGGATACACGTCTACCGGAGACGTCATCTGTTCTCCGTGTGGTCCCGGAACATATTCTCACACCGTCTCTTCCACAGATAAATGCGAACCCGTCGTAACCAGCAATACATTTAACTATATCGATGTGGAAATTAACCTGTATCCAGTCAACGACACATCGTGTACTCGGACGACCACTACCGGTCTCAGCGAATCCATCTCAACGTCGGAACTAACTATTACCATGAATCATAAAGATTGTGATCCAGTCTTTCGTGCAGAATACTTCTCTGTCCTTAATAATGTAGCAACTTCAGGATTCTTTACAGGAGAAAATAGATATCAGAATACTTCAAAGATATGTACTCTGAATTTCGAGATTAAATGTAACAACAAAGATTCATCTTCCAAACAGTTAACGAAAACAAAGAATGATACTATCATGCCGCATTCAGAGACGGTAACTCTAGTGGGCGACTGTCTATCTAGCGTCGACATCTACATACTATATAGTAATACCAATACTCAAGACTACGAAAATGATACAATCTCTTATCATATGGGTAATGTTCTCGATGTCAATAGCCATATGCCCGCTAGTTGCGATATACATAAACTGATCACTAATTCCCAGAATCCCACCCACTTATAGTAAGTTTTTTTACCTATAAATAATAAATACAATAATTAATTTCTCGTAAAAGTAGAAAATATATTCTAATTTATTATATGGTAAGAAAGTAGAATCATCTAGAACAGTAATCAATCAATAGCAATCATGAAACAATATATTGTCCTGGCATGCATGTGCCTAGTGGCAGCTGCTATGCCTACTAGTCTTCAACAATCTTCATCCTCGTGTACTGAAGAAGAAAACAAACATCATATGGGAATCGATGTTATTATCAAAGTCACAAAGCAAGACCAAACACCGACCAATGATAAGATTTGTCAATCCGTAACGGAAGTTACAGAGACCGAAGATGATGAGGTATCCGAAGAAGTTGTAAAAGGAGATCCCACCACTTATTACACTATCGTCGGTGCGGGTCTTAACATGAACTTTGGATTCACCAAATGCCCAAAGATTTCATCCATCTCCGAATCCTCTGATGGAAACACTGTGAATACTAGATTGTCCAGCGTGTCACCGGGACAAGGTAAGGACTCTCCCGCGATCACGCGTGAAGAAGCTCTGGCTATGATCAAAGACTGTGAGATGTCTATCGACATCAGATGTAGCGAAGAAGAGAAAGACAGTGACATCAAGACCCATCCAGTACTTGGGTCTAACATCTCACATAAGAAAGTGAGTTACAAAGATATCATCGGTTCAACGATCGTTGATACAAAATGTGTCAAGAACCTAGAGTTTAGCGTACGTATCGGAGACATGTGTGAGGAATCATCTGAACTTGAAGTCAAGGATGGATTCAAGTATGTCGACGGATCGGCATCTGAAGGTGCAACCGATGATACTTCACTCATCGATTCAACAAAACTCAAAGCATGTGTCTGAATCGATAACTCTATTCATCTGAAAATGGATGAGTTGGGTTAATCGAACGATTCAGACACCGCACCACGAATTAAAAAAGACCGGGCACTATATTCCGGTTTGCAAAACAAAAATATTTAACTACATTCACAAAAAGTTACCTCTCGTTACTTCTTCTTTCTGTTTCAATATGTGATACGATATGATCACTATTCGTATTCTCTTGGTCTCATAAAAAAGTTTTACAAAAAAAAAAAAAAAAATATTTTTATTCTCTTTCTCTCTTCGATGGTCTCACAAAAATATTAAACCTCTTTCTGATGTCTCAACTATTTCGTAAACGATAACGTCCAACAATATATTCTCGTAGAGCTTATCAACATCCTTATACCAATCTAGGTTGTCAGACAATTGCATCATAAAATAATGTTTATAATTTACACGTTAACATCATATAATAAACGTATATAGTTAATATTTTTGGAATATAAATGATCTGTAAAATCCATGTAGGGGACACTGCTCACGTTTTTTCTCTAGTACATAATTTCACACAAGTTTTTATACAGACAAATTAATTCTCGTCCATATATTTTAAAACATTGACTTTTGTACTAAGAAAAATATCTTGACTAACCATCTCTTTCTCTCTTCGATGGGTCTCACAAAAATATTAAACCTCTTTCTGATGGAGTCGTAAAAAGTTTTTATCCTTTCTCTCTTCGATAGGTCTCACAAAAATATTAAACCTCTTTCTGATGGTCTCTATAAACGATTGATTTTTCTTACCCTCTAGAGTTTCCTACGGTCGTGGGTCACACATTTTTTTCTAGACACTAAATAAAATAGTAAAAT
+>MPOX_ITR2#UNKNOWN
+GATAGATCGAAAAAAGCCACTAATAAAAACAGTTGGTTAATTACTTCAGGCTTTAGACTACAAAAATGGTTCGATAGCGAAGATTGTATAATTTATCTCAGATCTTTAGTTAGAAGAATGGAAGACAGTAACAAAAACAGTAAAAAAACTTAGTACTTAGATATCGAAAAAATATATTTTTGTAGACTCTTGAGAATAGAAGGAAAACATGTACATAATTATAAAAAATGAAAATCAATGGCGAATAAGACAGTGCGATTCGCACCATGGAGTCGGTAGATTTCATGGCTGTCGATGAGCAGTTTCACGACGACCTCGATCTTTGGTCATTATCTTTGGTAGATGATTATAAAAAACATGGATTAGGTGTTGACTGTTATGTTCTAGAACCAGTTGTTGACAGGAAAATATTTGATAGATTTCTCCTTGAACCAATTTGTGATCCTGTAGATGTTCTGTATGATTATTTTAGGATTCATAGAGATAATATTGATCAGTATATAGTAGATAGACTGTTTGCATATATTACATATAAAGATATTATATCTGCATTAGTGTCAAAGAATTATATGGAAGATATTTTCTCTATAATTATTAAGAATTGTAATTCTGTGCAAGATCTCTTACTTTACTATCTATCTAATGCATATGTAGAAATAGACATTGTTGATCTTATGGTAGATCATGGGGCTGTAATATATAAAATAGAATGCTTGAATGCCTATTTTAGGGGAATATGTAAAAAGGAAAGTAGTGTTGTTGAGTTTATTTTGAATTGTGGTATCCCAGATGAAAATGATGTTAAATTAGATCTATATAAAATAATTCAGTATACTAGGGGATTCCTTGTAGATGAACCCACAGTATTAGAAATTTATAAGCTTTGTATCCCATATATTGAAGATATCAATCAACTAGATGCTGGTGGAAGGACCTTGCTTTATCGCGCTATCTATGCAGGTTATATAGATTTAGTATCATGGCTATTAGAAAATGGAGCAAATGTCAACGCAGTAATGAGTAATGGATATACATGTCTTGACGTGGCCGTGGATAGGGGATCTGTCATCGCCCGTAGGGAAGCACATCTTAAAATATTAGAAATATTGCTTAGAGAACCATTGTCTATTGACTGTATAAAATTAGCTATACTTAATAATACAATTGAAAACCATGATGTGATAAAGCTCTGTATCAAGTATTTTATGATGGTAGATTATTCACTTTGTAATGTGTATGCATCATCACTCTTTGATTATATAATTGATTGTAAACAAGAATTGGAGTACATTAGGCAGATGAAAATTCATAATACAACCATGTATGAGTTAATCTATAATAGAGACAAAAACAAGCATGCTTCCCATATTCTACATAGGTATTCTAAACATCCAGTTTTGACACAGTGTATCACTAAAGGATTCAAGATTTACACAGAAGTAACCGAGCAGGTCACTAAAGCTCTAAACAGACGTGCTCTAATAGATGAGATAATAAACAATGTATCAACTGATGACAATCTCCTATCAAAACTTCCATTAGAAATTAGGGATCTAATTGTTTCACAAGCTGTCATATAGAGTTCTATCCACCCACCTTTCTTGAAATGAGTTAATAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTAAGTCATAAGTTAGTTTATAGTCTAACACTTCTAATTTTTATACCTTGATCTTTTTCTCTAATTATGAAAAAGTAAATCATTATGAAGATGGATGAAATGGACGAGATTGTGCGCATCGTTAACGATAGTATGTGGTACGTACCTAACGCATTTATGGACGACGGTGATAATGAAGGTCACATTTCTGTCAATAATGTCTGTCATATGTATCTCGCATTCTTTGATGTGGATATATCATCTCATCTGTTTAAATTAGTTATTAAACACTGCGATCTGAATAAACGACTAAAATGTGGTAACTCTCCATTACATTGCTATACGATGAATACACGATTTAATCCATCTGTATTAAAGATATTGTTACGCCACGGCATGCGTAACTTTGATAGCAAGGATAAAAAAGGACATATTCCTCTACACCACTATCTGATTCATTCACTATCAATCGATAACAAGATCTTTGATATACTAACGGACCCCATTGATGACTTTAGTAAATCATCCGATCTATTGCTGTGTTATCTTAGATATAAATTCAATGGGAGCTTAAACTATTACGTTCTGTACAAATTATTGACTAAAGGATCTGACCCTAATTGCGTCGATGAGGATGGACTCACTTCTCTTCATTACTACTGTAAACACATATCCGCGTTCCACGAAAGCAATTATTACAAGTCAAAGAGTCACACTAAGATGCGAGCTGAGAAGCGATTCATCTACGCGATAATAGATCATGGAGCAAACATTAACGCGGTTACGAAAATCGGAAATACGCCGTTACACACTTACCTTCAACAGTATACCAAACATAGTCCTCGTGTGGTGTATGCTCTTTTATCTCGAGGAGCCGATACGAGGATACGTAATAATCTTGATTGTACACCCATCATGGAATACATAAAGAACGATTGTGCAACAGGTCATATTCTCATAATGTTACTCAATTGGCACGAACAAAAATACGGGAAATTACAAAAGGAAGAAGGACAACATCTACTTTATCTATTCATAAAACATAATCAAGGATATGGAAGTCGCTCTCTCAATATACTACGGTATCTACTAGATAGATTCGACATTCAGAAAGACGAATACTATAATACAATGACTCCTCTTCATACCGCCTTCCAGAATTGCAATAACAATGTTGCCTCATACCTCGTATACATCGGATACGACATCAACCTTCCGACTAAAGACGATAAGACAGTATTCGACTTGGTGTTTGAAAACAGAAACATTATATACAAGGCGGATGTCGTTAATGACATTATCCACCACAGACTGAAAGTATCTCTACCTATGATTAAATCGTTGTTCTACAAGATGTCGGAGTTCTCTCCCTACGACGATCACTACGTAAAGAAGATAATAGCCTACTGCCTATTAAGGGACGAGTCATTTGCGGAACTACATACTAAATTCTGTTTAAACGAGGACTATAAAAGTGTATTTATGAAAAATATATCATTCGATAAGATAGATTCCATCATCGAAAAATGTAGTCGTGACATAAGTCTCCTCAAAGAGATTCGAATCTCAGACACCGACTTGTATACGGTATTGAGAACAGAAGACATCCGGTATCACACATATCTCGAAGCCATACATTCAGACAAACGCATTTCATTTCCCATGTACGACGATCTCATAGAACAGTGTCATCTATCGATGGAGCATAAAAGTAAACTCGTCGACAAAGCACTCAATAAATTAGAGTCTACCATCGATAGTCAATCTAGACTATCGTATTTGCCTCCGGAAATTATGCGCAATATCATAACCAAGCTAAGCGACTACCATCTAAACAGTATGTTGTACGGAAAGAACCATTACAAATATTATCCATGATAGAAAGAAAATATTTAAAAAATAATCTATATGATTGGAGAAGTAGGAAACAAACAGTAACAAGACGACGATTACTACATTATTAAATCATGAGGTCCGTATTATACTCGTATATATTGTTTCTCTCATGTATAATAATAAACGGAAGAGATATAGCACCACATGCACCATCCAATGGAAAGTGTAAAGACAACGAATACAGAAGCCGTAATCTATGTTGTCTATCGTGTCCTCCGGGAACTTACGCTTCCAGATTATGTGATAGCAAGACTAATACACAATGTACACCGTGTGGTTCGGATACCTTTACATCTCACAATAATCATTTACAGGCTTGTCTAAGTTGTAACGGAAGATGTGATAGTAATCAGGTAGAGACGCGATCGTGTAACACGACTCACAATAGAATCTGTGAATGCTCTCCAGGATATTATTGTCTTCTCAAAGGAGCATCAGGGTGTAGAACATGTATTTCTAAAACAAAGTGTGGAATAGGATACGGAGTATCCGGATACACGTCTACCGGAGACGTCATCTGTTCTCCGTGTGGTCCCGGAACATATTCTCACACCGTCTCTTCCACAGATAAATGCGAACCCGTCGTAACCAGCAATACATTTAACTATATCGATGTGGAAATTAACCTGTATCCAGTCAACGACACATCGTGTACTCGGACGACCACTACCGGTCTCAGCGAATCCATCTCAACGTCGGAACTAACTATTACCATGAATCATAAAGATTGTGATCCAGTCTTTCGTGCAGAATACTTCTCTGTCCTTAATAATGTAGCAACTTCAGGATTCTTTACAGGAGAAAATAGATATCAGAATACTTCAAAGATATGTACTCTGAATTTCGAGATTAAATGTAACAACAAAGATTCATCTTCCAAACAGTTAACGAAAACAAAGAATGATACTATCATGCCGCATTCAGAGACGGTAACTCTAGTGGGCGACTGTCTATCTAGCGTCGACATCTACATACTATATAGTAATACCAATACTCAAGACTACGAAAATGATACAATCTCTTATCATATGGGTAATGTTCTCGATGTCAATAGCCATATGCCCGCTAGTTGCGATATACATAAACTGATCACTAATTCCCAGAATCCCACCCACTTATAGTAAGTTTTTTTACCTATAAATAATAAATACAATAATTAATTTCTCGTAAAAGTAGAAAATATATTCTAATTTATTATATGGTAAGAAAGTAGAATCATCTAGAACAGTAATCAATCAATAGCAATCATGAAACAATATATTGTCCTGGCATGCATGTGCCTAGTGGCAGCTGCTATGCCTACTAGTCTTCAACAATCTTCATCCTCGTGTACTGAAGAAGAAAACAAACATCATATGGGAATCGATGTTATTATCAAAGTCACAAAGCAAGACCAAACACCGACCAATGATAAGATTTGTCAATCCGTAACGGAAGTTACAGAGACCGAAGATGATGAGGTATCCGAAGAAGTTGTAAAAGGAGATCCCACCACTTATTACACTATCGTCGGTGCGGGTCTTAACATGAACTTTGGATTCACCAAATGCCCAAAGATTTCATCCATCTCCGAATCCTCTGATGGAAACACTGTGAATACTAGATTGTCCAGCGTGTCACCGGGACAAGGTAAGGACTCTCCCGCGATCACGCGTGAAGAAGCTCTGGCTATGATCAAAGACTGTGAGATGTCTATCGACATCAGATGTAGCGAAGAAGAGAAAGACAGTGACATCAAGACCCATCCAGTACTTGGGTCTAACATCTCACATAAGAAAGTGAGTTACAAAGATATCATCGGTTCAACGATCGTTGATACAAAATGTGTCAAGAACCTAGAGTTTAGCGTACGTATCGGAGACATGTGTGAGGAATCATCTGAACTTGAAGTCAAGGATGGATTCAAGTATGTCGACGGATCGGCATCTGAAGGTGCAACCGATGATACTTCACTCATCGATTCAACAAAACTCAAAGCATGTGTCTGAATCGATAACTCTATTCATCTGAAAATGGATGAGTTGGGTTAATCGAACGATTCAGACACCGCACCACGAATTAAAAAAGACCGGGCACTATATTCCGGTTTGCAAAACAAAAATATTTAACTACATTCACAAAAAGTTACCTCTCGTTACTTCTTCTTTCTGTTTCAATATGTGATACGATATGATCACTATTCGTATTCTCTTGGTCTCATAAAAAAGTTTTACAAAAAAAAAAAAAAAAATATTTTTATTCTCTTTCTCTCTTCGATGGTCTCACAAAAATATTAAACCTCTTTCTGATGTCTCAACTATTTCGTAAACGATAACGTCCAACAATATATTCTCGTAGAGCTTATCAACATCCTTATACCAATCTAGGTTGTCAGACAATTGCATCATAAAATAATGTTTATAATTTACACGTTAACATCATATAATAAACGTATATAGTTAATATTTTTGGAATATAAATGATCTGTAAAATCCATGTAGGGGACACTGCTCACGTTTTTTCTCTAGTACATAATTTCACACAAGTTTTTATACAGACAAATTAATTCTCGTCCATATATTTTAAAACATTGACTTTTGTACTAAGAAAAATATCTTGACTAACCATCTCTTTCTCTCTTCGATGGGTCTCACAAAAATATTAAACCTCTTTCTGATGGAGTCGTAAAAAGTTTTTATCCTTTCTCTCTTCGATAGGTCTCACAAAAATATTAAACCTCTTTCTGATGGTCTCTATAAACGATTGATTTTTCTTACCCTCTAGAGTTTCCTACGGTCGTGGGTCACACATTTTTTTCTAGACA

assets/lib/varv_repeats_lib.fasta

@@ -0,0 +1,6 @@
+>VARV_ITR#UNKNOWN
+CATTCTGATGCATCAACTATTTCTTAAACAATAACGTTCAACAACATATACTCTCGAGCTTATCAACATCCCCTATGTCCCAACTAGGTTACCAAACAATTGTATATCATAAAATAATGTTTATAATTTACACGTTAAAATCATATAATAAAACGTAGATCGTATAATATTTTTTGGTATATAAATGATCTAGTAAAATCCATGTAGGGGATACTGTTCACGTTTTTTGGTACAAAATTTCTCACAAGTTTTTATACAGACAAATTCTTGTCCATATATTTTAAAACATTGACTTTTGCACTAAGAAAAATATATAGACTAACTATCTCTTTCTCTCTTCGATGGTCTCACAAAAATATTAAACCTCTTTCTGATGGAGTCGTAAAAAGTTTTATCTCTTTCTCTCTTCGATGGTCTCACAAAAATATTAAACCTCTTTCTGATGGAGTCGTAAAAAGTTTTATCTCTTTCTCTCTTCGATGGTCTCACAAAAATATTAAACCTCTTTCTGATGGAGTCGTAAAAAGTTTTATCTCTTTCTCTCTTCGATGGTCTCACAAAAATATTAAACCTCTTTCTGATGGAGTCGTAAAAAGTTTTATCTCTTTCTCTCTTCGATGGTCTCACAAAAATATTAAACCTCTTTCTGATGGTCTCTATAAAGCGATTGATTTTTTTACCCTCTAGAGTTTCCTACAGTCGTGGGTCACACATTTTTTTCTAGACAC
+>VARV_AT_repeat_region#UNKNOWN
+ATATATATATATATATATATATATATATATATATATATAT
+>VARV_T_repeat_region#UNKNOWN
+TTTTTTTTTT