[DOCKTESTERS] DKFZ bias filter docker

[Denis Yuen]

Hi, 
Looks good! I've done a test run and it looks like all the plumbing is functional. 
I've also created a pull request with an example test json file (works with an upcoming version of dockstore in test). 
________________________________________
From: Ivo Buchhalter [i.buchhalter at dkfz-heidelberg.de]
Sent: November 16, 2016 8:33 AM
To: Denis Yuen; Buchhalter, Ivo
Cc: docktesters at lists.icgc.org; Werner, Johannes; Prinz, Manuel; Schlesner, Matthias
Subject: Re: [DOCKTESTERS] DKFZ bias filter docker

Dear all,

Thanks to the big help from Johannes and Manuel we have finally a
running version of the DKFZ bias filter on Dockstore. You can find it
here: https://dockstore.org/containers/quay.io/jwerner_dkfz/DKFZBiasFilter

Please be aware that currently the json overwrites the default values so
you will have to make sure to replace them (see comment at the bottom of
the page).

If you have any questions let me/ Johannes know.

Thanks,
Ivo


On 10/26/2016 05:04 PM, Denis Yuen wrote:
> Hi,
> I think next week should be sufficient, thanks for the update!
>
> ________________________________________
> From: Buchhalter, Ivo [i.buchhalter at Dkfz-Heidelberg.de]
> Sent: October 26, 2016 9:32 AM
> To: Denis Yuen
> Cc: Buchhalter, Ivo; docktesters at lists.icgc.org; Werner, Johannes; Prinz, Manuel; Schlesner, Matthias
> Subject: Re: [DOCKTESTERS] DKFZ bias filter docker
>
> Hi Denis,
>
> Unfortunately Manuel, who was supposed to help us to fix the docker fell sick. He will be back by the mid of next week. Will it be sufficient it we submit our docker by the end of next week or should we try to start working on it (probably with your help?).
>
> Thanks,
> Ivo
>
>
>
>> On 19 Oct 2016, at 21:33, Denis Yuen <Denis.Yuen at oicr.on.ca> wrote:
>>
>> Hi,
>>
>> Thanks, this definitely helps to make it more clear.
>> I think this will give us enough information for us to start working on a CWL descriptor or to assist one being written.
>>
>> ________________________________________
>> From: Ivo Buchhalter [i.buchhalter at dkfz-heidelberg.de]
>> Sent: October 19, 2016 2:19 AM
>> To: Denis Yuen; Ivo Buchhalter; docktesters at lists.icgc.org
>> Cc: Werner, Johannes; prinz; Schlesner, Matthias
>> Subject: Re: [DOCKTESTERS] DKFZ bias filter docker
>>
>> Hi Denis,
>>
>> Sorry for the missing information. I updated the README in the
>> repository. I hope things are more clear now.
>>> 1) How does this relate to the existing dkfz workflow? ( https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows ) Is this a step that follows that workflow or is this a portion of that workflow that has been split out?
>> The filter is part of the DKFZ workflow. Since the other workflows don't
>> use similar filters the DKFZ stand alone filter was run on the complete
>> data set after merging the calls (only somatic SNV calls).
>>> 2) Could we get a readme that describes how to use this?
>> I updated the README. I hope it's more clear now.
>>> 3) Do you have some non-confidential small test data that we can use to run/test this quickly before running a real donor through this?
>> I will check if we can provide this later but the filter generally runs
>> only a couple of minutes (on a normal somatic "PASS" vcf with <= 10 000
>> variants).
>>
>> Best,
>> Ivo
>>
>>
>>> Thanks!
>>>
>>> ________________________________________
>>> From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Ivo Buchhalter [i.buchhalter at dkfz-heidelberg.de]
>>> Sent: October 18, 2016 3:06 AM
>>> To: docktesters at lists.icgc.org
>>> Cc: Werner, Johannes; prinz; Schlesner, Matthias
>>> Subject: [DOCKTESTERS] DKFZ bias filter docker
>>>
>>> Dear dockertesters,
>>>
>>> I was told to contact you regarding the DKFZ bias filter docker. The
>>> docker is basically ready and it also passed internal testing. The
>>> scripts and Dockerfile can be found here:
>>> https://github.com/eilslabs/DKFZBiasFilter
>>> Johannes and Manuel (CCed) have been working on bringing it into
>>> Dockstore (they ran into a NFS problem). Johannes is currently on
>>> vacation (until October 23rd).
>>> Please let me know if it is sufficient to have the docker available on
>>> Dockstore some time next week. Alternatively it might be possible that
>>> you work with the scripts and Dockerfile on GitHub. If none of this
>>> works I (or probably Manuel) can also try to get it running on Dockstore
>>> some time later this week.
>>>
>>> Best,
>>> Ivo
>>>
>>> PS: Sorry to the DKFZ people the email before bounced back because the
>>> link of the email address on the Wiki had a typo.
>>> _______________________________________________
>>> docktesters mailing list
>>> docktesters at lists.icgc.org
>>> https://lists.icgc.org/mailman/listinfo/docktesters
>> On 10/18/2016 05:38 PM, Denis Yuen wrote:
>>> Hi,
>>>
>>> Thanks for the heads-up, we can probably help out with writing the CWL descriptor for this, but I do have a few questions.
>>>
>>> 1) How does this relate to the existing dkfz workflow? ( https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows ) Is this a step that follows that workflow or is this a portion of that workflow that has been split out?
>>> 2) Could we get a readme that describes how to use this?
>>> 3) Do you have some non-confidential small test data that we can use to run/test this quickly before running a real donor through this?
>>>
>>> Thanks!
>>>
>>> ________________________________________
>>> From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Ivo Buchhalter [i.buchhalter at dkfz-heidelberg.de]
>>> Sent: October 18, 2016 3:06 AM
>>> To: docktesters at lists.icgc.org
>>> Cc: Werner, Johannes; prinz; Schlesner, Matthias
>>> Subject: [DOCKTESTERS] DKFZ bias filter docker
>>>
>>> Dear dockertesters,
>>>
>>> I was told to contact you regarding the DKFZ bias filter docker. The
>>> docker is basically ready and it also passed internal testing. The
>>> scripts and Dockerfile can be found here:
>>> https://github.com/eilslabs/DKFZBiasFilter
>>> Johannes and Manuel (CCed) have been working on bringing it into
>>> Dockstore (they ran into a NFS problem). Johannes is currently on
>>> vacation (until October 23rd).
>>> Please let me know if it is sufficient to have the docker available on
>>> Dockstore some time next week. Alternatively it might be possible that
>>> you work with the scripts and Dockerfile on GitHub. If none of this
>>> works I (or probably Manuel) can also try to get it running on Dockstore
>>> some time later this week.
>>>
>>> Best,
>>> Ivo
>>>
>>> PS: Sorry to the DKFZ people the email before bounced back because the
>>> link of the email address on the Wiki had a typo.
>>> _______________________________________________
>>> docktesters mailing list
>>> docktesters at lists.icgc.org
>>> https://lists.icgc.org/mailman/listinfo/docktesters