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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
MIT License
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ruamel - fix ChIPtests #966

Closed WardDeb closed 6 months ago

WardDeb commented 6 months ago

Should take care of the pytest issues with SEACR runs, and all the ones where the jobcount is also aberrant. ruamel is not an explicit dependency yet. Testing wether this should be the case.

WardDeb commented 6 months ago

I did run into something that I think is a bug, running ChIP-seq without a sampleSheet now errors out, this wasn't the case in 2.7.2, I've added a test for this, but the bug itself is not fixed yet.

○ → ChIP-seq -d bam_input/ --snakemakeOptions "--dryrun --conda-prefix /tmp -q " org.yaml chipdict.yaml

---- This analysis has been done using snakePipes version 2.7.3 ----
/localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/workflows/ChIP-seq/internals.snakefile:143: UserWarning: 6 out of 6 have a matching control 
  warnings.warn( str(len(chip_samples_w_ctrl)) + " out of " + str(len(chip_samples)) + " have a matching control ")
NameError in line 160 of /localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/shared/rules/ChIP_peak_calling.snakefile:
name 'isMultipleComparison' is not defined
  File "/localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/workflows/ChIP-seq/Snakefile", line 43, in <module>
  File "/localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/shared/rules/ChIP_peak_calling.snakefile", line 160, in <module>
Error: snakemake returned an error code of 1, so processing is incomplete!
katsikora commented 6 months ago

Thanks a lot for your help!

katsikora commented 6 months ago

I did run into something that I think is a bug, running ChIP-seq without a sampleSheet now errors out, this wasn't the case in 2.7.2, I've added a test for this, but the bug itself is not fixed yet.

○ → ChIP-seq -d bam_input/ --snakemakeOptions "--dryrun --conda-prefix /tmp -q " org.yaml chipdict.yaml

---- This analysis has been done using snakePipes version 2.7.3 ----
/localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/workflows/ChIP-seq/internals.snakefile:143: UserWarning: 6 out of 6 have a matching control 
  warnings.warn( str(len(chip_samples_w_ctrl)) + " out of " + str(len(chip_samples)) + " have a matching control ")
NameError in line 160 of /localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/shared/rules/ChIP_peak_calling.snakefile:
name 'isMultipleComparison' is not defined
  File "/localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/workflows/ChIP-seq/Snakefile", line 43, in <module>
  File "/localenv/deboutte/anaconda/miniconda/envs/snakepipes_dev/lib/python3.9/site-packages/snakePipes/shared/rules/ChIP_peak_calling.snakefile", line 160, in <module>
Error: snakemake returned an error code of 1, so processing is incomplete!

I'll take care of that on Monday :+1:

katsikora commented 6 months ago

Feel free to merge as it is, it looks great!