Annotation specified by user needs to be implemented

[nluu1]

Currently:

• The snpeff_annotate.sh allows user to specify: -d: the database -i: the input folder containing the files -o: the output folder

• The command looks like this:

  ./resources/snpeff_annotate.sh -d <database> -i <input folder containing vcf files> -o <output folder>

• The script and command have been implemented into Lloyd's workflow within the annotation.py but the database is being hard-coded into the script (i.e. "HsNRC-1").

• Eventually, we wanted to automatically queue the database from the workflow (if the database is not available, create new one) and be implemented into the scripts in annotation.py.

• I'm working on implementing the database creation, so I'll get back with an updated shell script.

[LloydJonesIII]

resources/snpeff_annotate.sh: line 44: /pH_Run/assembly/results/annotation/_final_variants_annotated.vcf: No such file or directory snpEff ann -no-downstream -no-upstream -c resources/SnpEff/snpEff.config HsNRC-1 /pH_Run/assembly/results/final_vcf/_final_variants.vcf > /pH_Run/assembly/results/annotation/_final_variants_annotated.vcf -s /pH_Run/assembly/results/annotation/_summary.html -csvStats /pH_Run/assembly/results/annotation/*_annotated.csv

• found this new error don't know how to fix

[nluu1]

resources/snpeff_annotate.sh: line 44: /pH_Run/assembly/results/annotation/final_variants_annotated.vcf: No such file or directory snpEff ann -no-downstream -no-upstream -c resources/SnpEff/snpEff.config HsNRC-1 /pH_Run/assembly/results/final_vcf/final_variants.vcf > /pH_Run/assembly/results/annotation/__final_variants_annotated.vcf -s /pH_Run/assembly/results/annotation/__summary.html -csvStats /pH_Run/assembly/results/annotation/*_annotated.csv

• found this new error don't know how to fix

• The error was due to a placement of a '/' before the specified folder in the 'annotation.py', resulting in the incorrect file path.

• /pH_Run this tells the VM to look for folder in the root directory, not current directory.

• The path for output folder and input folder should have been:

  pH_Run/assembly/results/annotation/

  or

  ./pH_Run/assembly/results/annotation

• The error has been resolved based on previous discussion.

[nluu1]

@PhyloGrok @LloydJonesIII

• I have updated the snpeff_annotate.sh and implemented annotation_config.sh to recognize the reference data, input folder, output folder (assuming filepath are the same for all workflow).
• The annotation_config.sh is located in the resources/ folder
• Now, the command can be run like so

  /media/volume/sdb/resources/annotation_config.sh pH_Run

• the pH_Run is actually the $1 variable, where user specify their project name/folder so replace them accordingly.
• The output file is located in /media/volume/sdb/pH_Run/assembly/results/annotation/

Note:

• I am aware of the following error as the folder within the workflow is somewhat restrictive:

  /media/volume/sdb/resources/snpeff_annotate.sh: line 51: /media/volume/sdb/pH_Run/assemb
  ly/results/annotation/SRR9025118_final_variants_annotated.vcf: Permission denied
  snpEff ann -no-downstream -no-upstream -c /media/volume/sdb/resources/SnpEff/snpEff.conf
  ig GCF_004799605.1 /media/volume/sdb/pH_Run/assembly/results/final_vcf/SRR9025118_final_
  variants.vcf > /media/volume/sdb/pH_Run/assembly/results/annotation/SRR9025118_final_var
  iants_annotated.vcf -s /media/volume/sdb/pH_Run/assembly/results/annotation/SRR9025118_s
  ummary.html -csvStats /media/volume/sdb/pH_Run/assembly/results/annotation/SRR9025118_an
  notated.csv

• the command chown -R $USER:$USER $RESULT_PATH/annotation/ temporarily solve the issue by letting the current logged in user the permission to access the folder annotation and is implemented into annotation_config.sh. This works for exouser, but did not work for my account intern3.
• Please let me know once you have a chance to try the command /media/volume/sdb/resources/annotation_config.sh pH_Run

[nluu1]

@PhyloGrok @LloydJonesIII

• I have updated the snpeff_annotate.sh and implemented annotation_config.sh to recognize the reference data, input folder, output folder (assuming filepath are the same for all workflow).
• The annotation_config.sh is located in the resources/ folder
• Now, the command can be run like so

/media/volume/sdb/resources/annotation_config.sh pH_Run

...

• Please let me know once you have a chance to try the command /media/volume/sdb/resources/annotation_config.sh pH_Run

Updated 08/03/2023

• The updated annotation command looks like so:

$annotation_config.sh $1 snpeff_annotate.sh

• In summary, $1 is the project folder the user specify, i.e. pH_Run. The annotation config will create a resources/ folder within the project workflow /media/volume/sdb/pH_Run/assembly/resources/ and create necessary files within the folder to build the database and run the annotation. Currently, the annotation_config.sh and the snpeff_annotate.sh is located in /media/volume/sdb/resources/. With this file path, the successful annotation command looks like so:

  /media/volume/sdb/resources/annotation_config.sh pH_Run /media/volume/sdb/resources/snpeff_annotate.sh 

• Eventually, we want the shell scripts to be in the GitHub repo, thus, I have moved the 2 files annotation_config.sh and snpeff_annotate.sh into the intern4 home so @LloydJonesIII can incorporate it into the workflow/repo. If the 2 files are in the same directory with the rest of python files (i.e. in same GitHub repo), it should look like this:

  ./annotation_config.sh pH_Run ./snpeff_annotate.sh 

[nluu1]

Run succesfully with Lloyd's workflow as 08/04/2023