Comments (15)
After fixing a bug in my calc_manta_vaf
script, it can now handle empty VCF files. So, there's no need for me to exclude empty VCF file from BEDPE processing. Note that svtools produces no output at all (rather than a header-only file), which might confuse downstream rules, but I think it's better to have an empty file than no file at all.
from lcr-modules.
Tagging @BrunoGrandePhD
from lcr-modules.
I'm realizing this may be a feature/bug of the configManta.py
part of Manta because the bam file is effectively ignored by the _manta_run
rule. Perhaps this is fixable by using the sample_bam as input to _manta_run
even though it doesn't actually use bam file directly.
from lcr-modules.
I suspect this has something to do with the checkpoints and a disconnect (i.e. variable mapping of file name) between what files are produced and what the inputs are.
from lcr-modules.
I'm also having trouble getting the manta module to complete bedpe generation and symlinking. Here you can see 103 rnaSV/*.vcf.gz
files, but only 98 bedpes.
lhilton@n105 /p/d/C/transcriptomes ❯❯❯ ls results/manta-1.0/03-bedpe/mrna--grch37/*/*.bedpe | wc -l
98
hilton@n105 /p/d/C/transcriptomes ❯❯❯ ls results/manta-1.0/99-outputs/bedpe/mrna--grch37/rnaSV/*.bedpe | wc -l
98
lhilton@n105 /p/d/C/transcriptomes ❯❯❯ ls results/manta-1.0/99-outputs/vcf/mrna--grch37/rnaSV/*.vcf.gz | wc -l
103
The output of snakemake -np _manta_all
is as follows:
Job counts:
count jobs
1 _manta_all
1 _manta_all_dispatch
1 _manta_run
3
I have one Manta job that keeps erroring out, so I expect one Manta run. However I also expected this to show jobs relating to bedpe generation. Is the issue here that the dispatch file already exists?
from lcr-modules.
I still need to look into the workflow not being triggered by newer input files, but the lower number of BEDPE files could be explained by the corresponding VCF files being empty. Could you check this?
from lcr-modules.
You are correct, there are five empty vcfs.
Now I see that you're removing empty VCFs from the bedpe targets. Is it possible to output a warning message about that?
from lcr-modules.
Absolutely, I can add a message. I might remove the checkpoint altogether because it seems to create more hassle than it's worth. I agree with Ryan: I suspect that it might account for the lack of re-runs when the upstream data is updated.
from lcr-modules.
@lkhilton: Did you re-run the module yet (presumably by deleting the output files)? If not, could you try deleting the "sentinel files" from the _manta_all_dispatch
rule? They're hidden (start with a period) in the 99-outputs/bedpe
subdirectory.
99-outputs/bedpe/{seq_type}--{genome_build}/.{tumour_id}--{normal_id}--{pair_status}.dispatched
from lcr-modules.
I wonder if it would be better if those files were not hidden. What is the rationale for that besides it making less "clutter" when we ls the directory?
from lcr-modules.
It was to minimize clutter, but I made that decision before I added the bedpe
and vcf
subdirectories in 99-outputs
. I've now moved to:
CFG["dirs"]["outputs"] + "dispatched/{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}.dispatched"
from lcr-modules.
As far as I can tell, I have successfully removed the checkpoint from the manta module. This should simplify everything.
from lcr-modules.
I can confirm that deleting the .dispatch
file initiates a re-run of manta on updated bam files.
from lcr-modules.
I've updated the _get_manta_files()
function to predict the output VCF files based on command-line options provided to Manta instead of waiting to see which ones are created by Manta. This should solve the issue reported here. I'll do a quick test before closing this issue.
https://github.com/LCR-BCCRC/lcr-modules/blob/dev-bgrande/modules/manta/1.0/manta.smk#L215-L252
from lcr-modules.
I believe this issue is gone now with version 2.0 of the manta module (without the checkpoint). If not, we can reopen this issue.
from lcr-modules.
Related Issues (20)
- Autorun basic tests on thanos when master updated
- Liftover issue regarding seq_type HOT 1
- SAGE doesn't handle `chr` prefixes correctly HOT 9
- StringTie HOT 1
- Oncopipe mis-handling unmatched normal IDs HOT 1
- Add unmatched samples to demo data HOT 1
- Update documentation HOT 1
- Documenting what each tool accomplishes
- Default unmatched normal bug HOT 2
- Harmonize all CNV caller modules and automatically convert seg files to projections HOT 2
- in_module is missing from some output rules
- Refactor the LymphGen module to run per-sample HOT 1
- Missing lymphgen script HOT 5
- Mutect2 edge case error HOT 2
- finalizing seg files have an issue with special genome builds HOT 3
- Ecotyper module needs wget conda environment HOT 2
- QC module does not report the per-chromosome coverage HOT 1
- Lofreq- no INDEL calling HOT 2
- ancient flag on all samples tsv prevents rerun of gistic2 HOT 1
- Strelka SomaticEVS filtering threshold HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from lcr-modules.