Add --fastq-end and use only tab files

[miguelpmachado]

Add --fastq-end option to allow user to use different fastq files ends besides sample.R1.fastq.gz sample.R2.fastq.gz
Use only tabular separated files instead of a mixture of tab and csv files

[miguelpmachado]

Hi @alialshahib,
I found your tool very useful. I made some changes in order to not restrict the fastq files ends to sample.R1.fastq.gz, etc., because for must labs, it is not the default files ends.
I also standardized the input files to tabular files.
Now I'm trying to figure out how to change your tool to add samples to ongoing surveillance projects. I sent an e-mail to ENA, and I'm hopping that they provide me useful information on how to do it.
Thank you very much for writing this tool.
Cheers,
Miguel

[alialshahib]

Hi Miguel Thank you for your comments. Im glad you are finding the tool useful. Please keep me updated on progress of changes. Regards Ali

…

________________________________ From: Miguel Machado [notifications@github.com] Sent: 29 January 2018 14:17 To: phe-bioinformatics/ena_submission Cc: Ali Al-Shahib; Mention Subject: Re: [phe-bioinformatics/ena_submission] Add --fastq-end and use only tab files (#1) Hi @alialshahib<https://github.com/alialshahib>, I found your tool very useful. I made some changes in order to not restrict the fastq files ends to sample.R1.fastq.gz, etc., because for must labs, it is not the default files ends. I also standardized the input files to tabular files. Now I'm trying to figure out how to change your tool to add samples to ongoing surveillance projects. I sent an e-mail to ENA, and I'm hopping that they provide me useful information on how to do it. Thank you very much for writing this tool. Cheers, Miguel — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#1 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AAj7PZv4U3kkFcTAfNg4OEMqYYFMv370ks5tPdLwgaJpZM4RwppW>. ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

[miguelpmachado]

Hi @alialshahib,
I added an option to allow checking samples info against ENA checklists

[alialshahib]

Great thanks.

…

________________________________________ From: Miguel Machado [notifications@github.com] Sent: 30 May 2018 14:27 To: phe-bioinformatics/ena_submission Cc: Ali Al-Shahib; Mention Subject: Re: [phe-bioinformatics/ena_submission] Add --fastq-end and use only tab files (#1) Hi @alialshahib<https://github.com/alialshahib>, I added an option to allow checking samples info against ENA checklists — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#1 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AAj7PVMiLLF2BVZmAyrrdT8nqRcJXR0Fks5t3p4ngaJpZM4RwppW>. ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************