Please see attachment

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I am a co-founder of Datirium, LLC. Datirium develops a CWL-based data analysis platform.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

Authors' response to reviews: (https://drive.google.com/file/d/1zUYVkKOGUBd7Od8rBWcvcTO2ARHee8gh/view?usp=sharing)

Most of my comments have been addressed and the manuscript is acceptable for publication. I have a few minor suggestions that do not require re-review. 1. Please provide a better explanation of how containers work. I couldn't quite follow dicussion on docker.yml and bioconda.yml Does PM4NGS uses pre-assembled docker containers or assembles them from bioconda or both? A few background sentences on what is bioconda and what is biocontainers and how they relate to docker will be helpful. 2. In supplementary tables, please provide a better explanation for steps: e.g. IGV tools make "TDF" What is it? Why is it needed, etc.

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I am a co-founder of Datirium, LLC. Datirium develops a CWL-based data analysis platform.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

Authors' response to reviews: Reviewer #1: Thanks for addressing my concerns. The paper looks ready to be published. Reviewer #2: Most of my comments have been addressed and the manuscript is acceptable for publication. I have a few minor suggestions that do not require re-review. 1. Please provide a better explanation of how containers work. I couldn't quite follow dicussion on docker.yml and bioconda.yml Does PM4NGS uses pre-assembled docker containers or assembles them from bioconda or both? A few background sentences on what is bioconda and what is biocontainers and how they relate to docker will be helpful. 2. In supplementary tables, please provide a better explanation for steps: e.g. IGV tools make "TDF" What is it? Why is it needed, etc.