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Snakemake version
Snakemake latest v6.15.5. But as well in v6.14.0 and v6.13.1.
Describe the bug
The code is not shown in the report generated after snakemake workflow completion in the case of a wrapper code, a script code. It is however correctly displayed when using the shell: directive. The problem was already mentioned on StackOverflow here and there and on Github by @SultanOrazbayev in #1109. The latter indicated that in v6.4.1 the problem did not exist.
Logs
No errors from the report command. The wrapper and script code appeared to be loaded.
$ snakemake --report
Building DAG of jobs...
Creating report...
Downloading resources and rendering HTML.
Loading wrapper code for rule bgzip
Loading script code for rule b
Report created: report.html.
* Remove the decode attributes of source files fix#1393
* Adding a test with report generation without md5sum check
* Formatting with black
* feat: Adding --cluster-cancel and --cluster-cancel-nargs (#1395)
* Adding support for --cluster-[m]cancel
* Adding support for --cluster-[m]cancel.
* Adressing points from code review
* [ci skip] fix typos
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
Co-authored-by: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Snakemake version
Snakemake latest
v6.15.5
. But as well inv6.14.0
andv6.13.1
.Describe the bug
The code is not shown in the report generated after snakemake workflow completion in the case of a wrapper code, a script code. It is however correctly displayed when using the
shell:
directive. The problem was already mentioned on StackOverflow here and there and on Github by @SultanOrazbayev in #1109. The latter indicated that inv6.4.1
the problem did not exist.Logs
No errors from the report command. The wrapper and script code appeared to be loaded.
Minimal example
A minimal example based on the comment of @SultanOrazbayev in #1109 (comment) is available as a gist:
For a faster version without wrapper installation, use:
To check whether the code is displayed requires however to:
report.html
bgzip
orb
in the graphAdditional context
snakemake/snakemake/report/__init__.py
Line 247 in 0246bc9
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