bpipe
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Bpipe - a tool for running and managing bioinformatics pipelines
some samples occur the questions below: ``` bpipe: line 762: 63827 Killed nohup bash -c "$LAUNCH_CMD" > /dev/null 2>&1 ``` is this related to the bpipe? thanks a lot.
I have working version of bpipe script that worked in versions 0.9.9.2 & 0.9.9.5. But when I ran it in bpipe 0.9.9.8, it had errors. It seems that the new...
I have the following code snippit, as per discussion at #248 ```groovy convert = { branch.name = "${branch.name}.convert" if(file(input).name.endsWith('.mnc')) { exec """ mincconvert -2 -clobber -compress 9 $input.mnc $output.mnc """...
Hello, I'm experimenting with bpipe version 0.9.9.7 and realized that when a folder in the path of collected files ends the same way as the collected files, bpipe confuses the...
Hi there, we realized that since release version 0.9.9.7, `forward input` seems to be ignored if run as the last step of a parallel branch. Consider this minimal example: ```...
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I have downloaded `mail.jar` and created ".bpipeconfig" file in my home directory and wrote : ``` notifications { smtp { to="[email protected]" host="smtp.163.com" secure=false username="bpipe_notification" password="my_password" // optional from="[email protected]" // optional,...
I have a pipeline file with the following run command: ``` run { "%_*" * [trim] + "%_*" * [align] + "%_*" * [removeSupplementary] + "%_*" * [removeDuplicates] + branches...
Right now I define a specific command to use extra memory in bpipe.config: ``` commands { mincbeast { memory="4G" // mincbeast uses 4G per run } } ``` This makes...