@AndreasHeger @sebastian-luna-valero I know I have sent you an email , but I thought that I would document this on GitHub so we have a record here.
I have been looking at pipeline testing and I have potentially found the issue with the readqc pipeline.
The pipeline.ini file needs to be updated using the following: /ifs/projects/adam/pipeline_testing/tests/test_readqc.dir/pipeline.yml
exportdir: export was missing from the pipeline.yml file.
I am also seeing pipeline_scrnaseqqc failures, but I think you mentioned that you would look into this andreas. If you don’t have time I am happy to look at this on Friday.
I am also seeing missing files when testing pipeline_intervals. The following files are missing:
test_intervals.dir/export/bed/neural-SMC3-R2.bed.gz,test_intervals.dir/export/meme/neural-SMC3-R1.meme/meme.txt,test_intervals.dir/export/bed/neural-SMC3-R1.bed.gz,test_intervals.dir/export/peaks/neural-SMC3-R2.peak.bed.gz,test_intervals.dir/export/meme/neural-SMC3-R2.meme/meme.txt,test_intervals.dir/export/peaks/neural-SMC3-R1.peak.bed.gz
Again, exportdir: export was missing from the pipeline.yml test file.
Acribbs
commented
6 years ago
@AndreasHeger @sebastian-luna-valero I know I have sent you an email , but I thought that I would document this on GitHub so we have a record here.
I have been looking at pipeline testing and I have potentially found the issue with the readqc pipeline.
The pipeline.ini file needs to be updated using the following: /ifs/projects/adam/pipeline_testing/tests/test_readqc.dir/pipeline.yml
exportdir: export was missing from the pipeline.yml file.
I am also seeing pipeline_scrnaseqqc failures, but I think you mentioned that you would look into this andreas. If you don’t have time I am happy to look at this on Friday.
I am also seeing missing files when testing pipeline_intervals. The following files are missing: test_intervals.dir/export/bed/neural-SMC3-R2.bed.gz,test_intervals.dir/export/meme/neural-SMC3-R1.meme/meme.txt,test_intervals.dir/export/bed/neural-SMC3-R1.bed.gz,test_intervals.dir/export/peaks/neural-SMC3-R2.peak.bed.gz,test_intervals.dir/export/meme/neural-SMC3-R2.meme/meme.txt,test_intervals.dir/export/peaks/neural-SMC3-R1.peak.bed.gz
Again, exportdir: export was missing from the pipeline.yml test file.