[Feature Request]: add back the Genbank output present in pLannotate

splaisan commented 1 year ago

What happened?

When I run pLannotate (v1.2.0) on the assembly, I get a genbank formatted file which is not produced when running the ONT workflow.

Is the nextflow pLannotate wrapper somehow adding-x, --no_gbk supresses GenBank output file to the command to not output Genbank?

Is it possible to tune some config file in order to get that key output as well using the wf-clone-validation?

End users do not want a BED file, they want a GB file which they can open in their plasmid manipulation software. thanks in advance

Another cool feature would be a static picture of the plasmid map (PDF or PNG), I cannot export one from the interactive report.

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

No response

Workflow Execution - CLI Execution Profile

None

Workflow Version

v0.3.1-g97e1eab

Relevant log output

I have only:

feature_table.txt
bc01.annotations.bed
bc01.final.fasta

sarahjeeeze commented 1 year ago

Hi, Thanks for your feedback. We will consider outputting the .gbk file in a future release.

ChristopherRichie commented 1 year ago

While I very much want a Genbank-compatible file (every time), I have to disagree about "end users do not want a bed file". I use the BED file to sketch out my features on IGV application (where Genbank files are not useful) when I am trying to interpret my CRAM/BAM files.

Please allow for either or both kinds of end points as options or produce both kinds of output by default.

sarahjeeeze commented 1 year ago

Yes, sorry for the delay we will add this shortly.

ChristopherRichie commented 1 year ago

thanks

From: Sarah Griffiths @.> Sent: Friday, September 1, 2023 11:25 AM To: epi2me-labs/wf-clone-validation @.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Comment @.> Subject: [EXTERNAL] Re: [epi2me-labs/wf-clone-validation] [Feature Request]: add back the Genbank output present in pLannotate (Issue #21)

Yes, sorry for the delay we will add this shortly.

- Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-clone-validation/issues/21#issuecomment-1702928120, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR4COQ5TFPCHZIYUJMIYNPTXYH43NANCNFSM6AAAAAAYUGPDVA. You are receiving this because you commented.Message ID: @.**@.>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

splaisan commented 1 year ago

Thanks a lot

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From: ChristopherRichie @.> Sent: Friday, September 1, 2023 5:34:39 PM To: epi2me-labs/wf-clone-validation @.> Cc: Stéphane Plaisance @.>; Author @.> Subject: Re: [epi2me-labs/wf-clone-validation] [Feature Request]: add back the Genbank output present in pLannotate (Issue #21)

thanks

From: Sarah Griffiths @.> Sent: Friday, September 1, 2023 11:25 AM To: epi2me-labs/wf-clone-validation @.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Comment @.> Subject: [EXTERNAL] Re: [epi2me-labs/wf-clone-validation] [Feature Request]: add back the Genbank output present in pLannotate (Issue #21)

Yes, sorry for the delay we will add this shortly.

- Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-clone-validation/issues/21#issuecomment-1702928120, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR4COQ5TFPCHZIYUJMIYNPTXYH43NANCNFSM6AAAAAAYUGPDVA. You are receiving this because you commented.Message ID: @.**@.>> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

— Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-clone-validation/issues/21#issuecomment-1702941611, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAGRTFAU52HN4WDI6RWFAV3XYH6A7ANCNFSM6AAAAAAYUGPDVA. You are receiving this because you authored the thread.Message ID: @.***>

sarahjeeeze commented 1 year ago

Hi, this is now available in the pre-release and will be in the next tagged version. No extra parameters are required, the gbk will just be in the output directory per sample.

splaisan commented 1 year ago

thanks a lot Sarah! very valuable to open the GB file in GUI apps and get a nice map quickly (or instance for PCR-design and cloning purposes) and also to submit it to databases

epi2me-labs / wf-clone-validation