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Hi Phil,
I've been trying to use `htseq_counts.cfmod` with the mouse genome `.gtf` file from `mm10`. In this gtf file the gene is marked by `gene_id` not `ID`. However, `ID` is hardcoded into the com…
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Could be cool to write a summary module for methylation data using [methylkit](https://code.google.com/p/methylkit/) (see [docs](https://github.com/al2na/methylKit/blob/master/vignettes/methylKit.pdf)…
ewels updated
9 years ago
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Currently, the downloads module takes URL and filename as parameters on the command line when called. It'd be better to do this as regular filenames in the run file - less parameters, also other modul…
ewels updated
9 years ago
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Deleting pipelines sometimes throws errors:
``` perl
Deleting jobs from Pipeline id trim_galore_1415031486
Use of uninitialized value $pipelinekey in string eq at /bi/apps/clusterflow/0.4_devel/sour…
ewels updated
9 years ago
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`cf --qstatall` currently produces a few hundred errors such as:
``` perl
Deep recursion on subroutine "CF::Headnodehelpers::parse_job_dependency_hash" at /bi/apps/clusterflow/0.4_devel/source/CF/Hea…
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Add command line option to use a custom run file filename. The current run file filenames are called `input_pipeline.run` (where `input` is the first input file filename and `pipeline` is the pipeline…
ewels updated
9 years ago
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Bismark methylation extrator module threw the following warning and later failed:
```
Reference found where even-sized list expected at /bi/apps/clusterflow/0.4_devel/modules/../source/CF/Helpers.pm …
ewels updated
9 years ago
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Remove the option to use `vf` for memory assignment. Always use `h_vmem` instead.
@stu2 - is this going to mess up your work flow at all, or is this ok?
ewels updated
9 years ago
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The gwcov option (#bismark_methXtract gwcov) tries to find scripts in your home directory and thus fails. Cheers, Felix
- Error! Can't find capture regions BED file - running without capture infor…
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Hi Phil, we recently had issues with CF runs failing for various reasons, probably mostly memory related issues. Once the jobs were killed there is no way of finding out what the job ID was and this m…