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wrapper code and script code not displayed in report but shell code is #1393

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cpauvert opened this issue Feb 11, 2022 · 1 comment · Fixed by #1404
Closed

wrapper code and script code not displayed in report but shell code is #1393

cpauvert opened this issue Feb 11, 2022 · 1 comment · Fixed by #1404
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bug Something isn't working

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@cpauvert
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cpauvert commented Feb 11, 2022

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.

Minimal example
A minimal example based on the comment of @SultanOrazbayev in #1109 (comment) is available as a gist:

git clone https://gist.github.com/3cdd652717ac36862497c797d80f1fae.git
cd 3cdd652717ac36862497c797d80f1fae
snakemake -c 1 --use-conda 
snakemake --report

For a faster version without wrapper installation, use:

git clone https://gist.github.com/3cdd652717ac36862497c797d80f1fae.git
cd 3cdd652717ac36862497c797d80f1fae
snakemake -c 1 test.vcf
snakemake --report

To check whether the code is displayed requires however to:

  1. open the report.html
  2. Click on the rule bgzip or b in the graph
  3. See if the code is displayed

Additional context

@cpauvert cpauvert added the bug Something isn't working label Feb 11, 2022
@cpauvert
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cpauvert commented Feb 15, 2022

No additionally relevant information appears when running snakemake --debug --verbose

cpauvert added a commit to cpauvert/snakemake that referenced this issue Feb 16, 2022
johanneskoester added a commit that referenced this issue Feb 18, 2022
* 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>
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