clusterflow
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ewels
A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
On our system we're using the newer [Lmod](https://lmod.readthedocs.io/en/latest/index.html) environment module system rather than the original environment modules. LMod is syntactically and API compatible with environment modules, but uses different back...
There's a mismatched bracket which stops the actual command and other relevant things being added to the SLURM submit if the custom command is used.
I currently have the `@max_time` set to `23:59:00` in my clusterflow.config file and I have changed cr_download.cfmod.pl to make the time equal to `num_files * 60` because my cluster is...
From an email: > When I try run the `samtools_sort_index` module on an unsorted BAM file it generates a `_srtd` and `_srtd.bai` files. Although these files contain the correct information,...
``` ====================================================================== Cluster Flow Pipeline: samtools_sort_index Submitted: 20 minutes, 5 seconds ago Working Directory: /bi/group/bioinf/Rachael_Huntly/Cufflinks_Analysis/Rachel_0_vs_8_hour Cluster Flow ID: samtools_sort_index_1485260139 Submitted Jobs: 17 Running Jobs: 8 Queued Jobs: 11 (resources) Completed...
I think that bioconda is capable of packaging perl packages too? Would be nice to add it if so.
- [x] Move the current coverage code out of `bismark_methXtract` module and in to own module. - [x] Move the genome wide coverage report stuff from `bismark_methXtract` and just run...
The code base and user base of Cluster Flow is expanding. Bundling everything with the core package is bulky, and makes it difficult for people to customise things without deviating...
RSeQC
Module for [RSeQC](http://rseqc.sourceforge.net/) perhaps? _Edit:_ This probably isn't a single module, rather a group of several: - [x] [rseqc_inner_distance](http://rseqc.sourceforge.net/#inner-distance-py) - [x] [rseqc_geneBody_coverage](http://rseqc.sourceforge.net/#genebody-coverage-py) - [x] [rseqc_read_GC](http://rseqc.sourceforge.net/#read-gc-py) - [x] [rseqc_junctions](http://rseqc.sourceforge.net/#junction-annotation-py) (`junctions_annotation.py` and...
One limitation of modules currently is that they typically only output one file type. Also, sample grouping information is lost. This is fine when, for example, an alignment module has...