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BIMSBbioinfo / pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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final report should not be rerun if addtional diffmeth comparisons are requested #133

Closed alexg9010 closed 6 years ago

alexg9010 commented 6 years ago

I just analysed the test data and when it was done I added a new comparison to treatment_groups.

This triggered the creation of a new diffmeth-report as expected, but also reinforced the creation of the final report for every sample.

alexg9010 commented 6 years ago

Upon closer investigation I got this job message:

Job 17: ----------  Calculating differential methylation.  ----------
Reason: Missing output files: 10_differential_methylation/0_2.deduped_diffmeth.bed, 10_differential_methylation/0_2.deduped_diffmethhyper.RDS, 10_differential_methylation/0_2.deduped_diffmethhypo.RDS, 10_differential_methylation/0_2.deduped_diffmeth.RDS

This is probably due to this line: https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/BSseq_pipeline.py#L202.

This can be removed now, since final report is independent from diffmeth report. DiffMeth report is triggered if treatment_groups are given: https://github.com/BIMSBbioinfo/pigx_bsseq/blob/master/BSseq_pipeline.py#L142-L144