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Hello,
While debugging the reason for a failing test for Bioconda Mintie (bioconda/bioconda-recipes#48862) I've found out that bpipe --help started returning status code 1 in version 0.9.12.
martin@tuxedo:/tmp/mintie/LinuxArtifacts/packages/noarch/fff$ bpipe --help
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
Bpipe Version 0.9.12 Built on Sun May 07 08:05:09 EEST 2023
usage: bpipe [run|test|debug|touch|execute] [options] <pipeline> <in1> <in2>...
retry [job id] [test]
remake <file1> <file2>...
resume
stop [preallocated]
history
log [-n <lines>] [job id]
jobs
checks [options]
override
status
cleanup
query <file>
preallocate
archive [--delete] <zip file path>
autoarchive
preserve
register <pipeline> <in1> <in2>...
diagram <pipeline> <in1> <in2>...
diagrameditor <pipeline> <in1> <in2>...
Options:
-a,--autoarchive <arg> clean up all internal files after run into given archive
-b,--branch <arg> Comma separated list of branches to limit execution to
-d,--dir <arg> output directory
-e,--env <arg> Environment to select from alternate configurations in
bpipe.config
-f,--filename <arg> output file name of report
-h,--help usage information
-l,--resource <resource=value> place limit on named resource
-L,--interval <arg> the default genomic interval to execute pipeline for (samtools
format)
-m,--memory <arg> maximum memory in MB, or specified as <n>GB or <n>MB
-n,--threads <arg> maximum threads
-p,--param <param=value> defines a pipeline parameter, or file of parameters via @<file>
-r,--report generate an HTML report / documentation for pipeline
-R,--report <arg> generate report using named template
-s,--source <arg> Load the given pipeline file(s) before running / executing
-t,--test test mode
-u,--until <arg> run until stage given
-v,--verbose print internal logging to standard error
-y,--yes answer yes to any prompts or questions
martin@tuxedo:/tmp/mintie/LinuxArtifacts/packages/noarch/fff$ echo $?
1
It was returning 0 in the previously used version (0.9.9).
Is this change intentional ?
Thank you!
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