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6. FAQ
Below you may find an answer to your question about mapache
.
You can see a list of the jobs that will be executed with the line
snakemake -n
and also print the command lines to be executed with
snakemake -n -p
See the information here
snakemake -R `snakemake --list-input-changes`
do not forget to add the --cores
or --jobs
and --profile
arguments depending on how you want to execute the jobs.
Similarly as above, you need to include the options --cores
or --jobs
and --profile
to the following line:
snakemake -n -R `snakemake --list-params-changes`
Q: I tweaked some parameters of the plots in the config file, but the plots in the report look the same as before. How can I fix that?
You first need to ask snakemake to re-create the plots, and then generate the report.
snakemake -R `snakemake --list-params-changes` --cores 1
snakemake --report
As it is common to make mistakes in both wet and dry labs, we highly recommend to adhere to meaningful names for the samples, libraries and ID columns of the samples files. This might be helpful in the case you spot an odd output (e.g., empty BAM files, high contamination, less reads than expected) due to different sources of errors (sample swaps, truncated input files, wrong paths).
We encourage you to make use of the dry runs (-n) and subsample a small number of reads to verify that a random subset of your reads are well mapped, but also to get familiar with the pipeline.
Finally, the report contains several statistics that are usually helpful to have a quick and first idea of the quality of the mappings.
Due to license restrictions, the mapache conda package cannot distribute and install GATK 3.8 directly (please note that GATK IndelRealigner used in the pipeline is not available in GATK >v4). To fully install GATK, you must download a licensed copy of GATK from the Broad Institute, and call “gatk-register,” which will copy GATK into your mapache conda environment:
# (download licensed copy of GATK)
gatk-register /path/to/GenomeAnalysisTK.jar
In short, you have
- to activate the conda environment containing GATK.
conda activate mapache
- type
gatk
to see if GATK is already registered. If you get the following output, you have to register GATK:
$ gatk3
GATK jar file not found. Have you run "gatk3-register"?
-
download the registration file from Broad Institute.
-
register GATK
gatk3-register GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2
When running the pipeline with rule-based conda environments (--use-conda), snakemake will create several envs that store different packages needed by the pipeline. In order to properly install GATK if you are using this, you will fist need to built the conda environments:
snakemake --use-conda --conda-create-envs-only --cores N
Where N is the number of CPUs you want to use (1 for only one core, all for all of them)
You then need to find which of these environments contains GATK:
$ grep -i gatk /path/to/mapache/.snakemake/conda/*.yaml
/path/to/mapache/.snakemake/conda/82f2bb3b7e488f30c27f6219ba709caf.yaml: - gatk = 3.8
and load the corresponding environment by copy-pasting it’s path (without the .yaml extension):
$ conda activate /path/to/mapache/.snakemake/conda/82f2bb3b7e488f30c27f6219ba709caf
Once this is done, you can install the licence with the command:
gatk3-register /path/to/GenomeAnalysisTK.jar
Welcome to Mapache's wiki! Got any question? Found a bug? Please open an issue.