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bpipe --help returns status code = 1 #292

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martin-g opened this issue Jul 2, 2024 · 0 comments
Open

bpipe --help returns status code = 1 #292

martin-g opened this issue Jul 2, 2024 · 0 comments

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@martin-g
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martin-g commented Jul 2, 2024

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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