gudeqing

Hi @sigve， will you check if the following arguments work as expected ？ --tumor_dp_min 5 \ --tumor_af_min 0.05 \ --tumor_dp_tag TDP \ --tumor_af_tag TAF \ --control_dp_tag NDP \ --control_af_tag NAF...

Hi, sigven, Nice to have it work properly now. By the way, here is a small script that helps to copy "DP/AF" in FORMAT to INFO field, However, I still...

Hi, @sigven , First, pcgr requires the user to provide tumor sample id, thus we could use this ID to differentiate tumor sample from normal sample. Second, in most times,...

So sorry for the late response. To the best of my understanding, mysql database is needed to be configured to support the cache function. [cromwell_mysql.pdf](https://github.com/broadinstitute/cromwell/files/9853162/cromwell_mysql.pdf)

Thanks, @freeseek , I see. Anyway, my solution is to make no default value for "Directory" input. From my own experiences, you should never expect WDL being perfect, haha.

@Manuel-DominguezCBG I am using an alternative image from goalconsortium/abra2:latest, with version 2.20

Hi, I think a good alternative way is to derive needed metrics using a small python script, it is fast and easy, such as: ``` for sample, task in bamdst_task_dict.items():...

I also got this same issue using the latest image using cwltool, and the reason is that the “/tmp” directory is replaced by cwltool

@lbergelson Hi, thank you for your kind reply. Following is the report of ValidateSamFile: Tool returned: 3 ERROR::RECORD_OUT_OF_ORDER:Record 86076959, Read name A00583:183:HLCWVDMXX:1:1114:30897:16579, The record is out of [coordinate] order, prior...