ONT_pilot_w_GDB_samples.md

@@ -356,19 +356,54 @@ vi config/CONFIG.yaml
 # Also, had to adjust the rules/ASSEMBLY_ANNOTATION_RULES, and the workflows/assembly.smk files
 # Adjusted the short-read "name" in the rules files from "NEB2_MG_S17" to "ONT3_MG_xx_Rashi_S11"
 # Adjusted the config file to run the first line before going on to the second line and further
-# Included the workflows as steps in the [CONFIG.YAML](url) file
-# steps: "mmseq metaT mapping binning taxonomy"
-steps: "assembly_annotation metaT"
-steps: "mapping mmseq binning taxonomy"
+# Included the workflows as steps in the [CONFIG.YAML](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/master/config/CONFIG.yamlurl) file
+
+steps: "assembly_annotation metaT mapping mmseq binning taxonomy"
 
 # Basecalling taking too long, so running separately
 # created a "basecalling_snakefile" and an associated launcher script "run_basecalling_snakemake.sh"
 cp src/snakemake_run_use_conda_FINAL.sh run_basecalling_snakemake.sh
 ./run_basecalling_snakemake.sh
+
+##### Running non-methylation-aware-basecalled results #####
+mv -vf results methylation_aware_results
+mkdir results 
+cp -vrf methylation_aware_results/basecalled_NO_MOD results/basecalled
+rm *.done
+
+# re-running the whole workflow for the non-methylation aware basecalled results
+./src/snakemake_run_use_conda_FINAL.sh    
+
+# issues with the "FLYE ASSEMBLY"
+# Error: https://github.com/fenderglass/Flye/issues/61
+# creating a new conda environment with the latest flye
+conda create -n flye flye
+conda activate flye
+conda env export > envs/flye_v2_7.yaml
+sed -i 's/=[^=]*//2g' envs/flye_v2_7.yaml
+
+# adjusted "rules/ASSEMBLY_ANNOTATION_RULES" to look for the new flye conda env
+# re-running with new 'flye' environment
+./src/snakemake_run_use_conda_FINAL.sh
 ```
 
+## Chapter IX - If it ain't broke, why fix it? Well, to beautify it!!
+- 2019_GDB data does not have any barcodes, unlike 2018 data which was multiplexed
+- So, it is essential to create a generic workflow that can be used with others that have barcodes
+- To improve this, we created the "WORKING_checkpoint_snakefile"
+- this includes the guppy basecalling, merging fastq(s) and creating "dummy" folders rules
+- Added new 'rule' and 'workflow' to the respective folders as follows, by adding the updated 'checkpoint' rules
+- files created are as below
+1. [rules/checkpoint_ASSEMBLY_ANNOTATION_RULES](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/checkpoint_snakefile/2019_GDB/rules/checkpoint_ASSEMBLY_ANNOTATION_RULES)
+2. [workflows/checkpoint_assembly_annotation.smk](https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/checkpoint_snakefile/2019_GDB/workflows/checkpoint_assembly_annotation.smk)
+
+cp updated_SNAKEFILE checkpoint_SNAKEFILE
+# edited the paths to the 'rules' and 'workflows' in the "checkpoint_SNAKEFILE", to include the above files 
+# test run the "checkpoint_SNAKEILF"
+snakemake -np -s checkpoint_SNAKEFILE --use-conda     # test-run seemed to work fine
+```
 
-## Chapter IX - The miscellaneous or nearly-forgotten side projects
+## Chapter X - The miscellaneous or nearly-forgotten side projects
 - Due to the multifaceted nature of the best, i.e. the modular workflow, we tested several aspects separately
 - For example: since we used two mappers bwa-mem and minimap for the reads, we binned each sample separtely based on the mapper
 - Additionally, we needed to merge bam files for the "hybrid"-binning, so we compared bins using [sourmash](https://github.com/dib-lab/sourmash) and compared assemblies using [quast](https://github.com/ablab/quast)