Generalities¶
Defining variables¶
As a general rules, any variable referenced in this documentation must be either:
- Defined in the yaml config file that is passed to snakemake by
--configfile - Defined directly in the snakemake command by
--config variable=$value
Logging functions¶
Archiving processes are defined in the file workflows/logging.rules. The variable logging_folder must be defined in the config.yaml or passed to snakemake with --config. Each time an effective snakemake run is started, a folder named with the current UTC datetime is created. A variable number of files will be copied there, so that replication of the run is possible:
- The snakefile passed to snakemake
- The config file
- The full command used, copied into the file
cmd.txt - The parameter files defining the SRA and the local samples, if they exist
The logs of every command run during the execution of the workflow will then be stored in this folder.
Determining sample names¶
Sample naming and matching to fastq files are handled in the file workflows/making_sample_dataset.rules.
Local samples¶
Local samples will be determined based on a tabulated file whose full path must be passed to the variable local_samples in the config.yaml or through --config on the snakemake command. It must contain at least two columns: SampleName and ScientificName.
| SampleName | ScientificName |
|---|---|
| S10 | Staphylococcus aureus |
| S1 | Staphylococcus aureus |
For each entry, there must be in the folder defined by the link_directory variable, two files (for paired reads) or only one (for single reads) whose filename starts by one and only one entry of the SampleName columns. For instance, the files S10_001_R1_L001.fastq.gz and S10_001_R2_L001.fastq.gz in the folder defined by the link_directory variable will be matched to the sample name S10. The matching is performed by using regular expressions to end the search at non alphanumeric characters or by the end of the word, thus the sample name S1 will actually not match S10_001_R1_L001.fastq.gz nor S10_001_R2_L001.fastq.gz.
If needed, an OldSampleName column can be added to the file, when the read filenames and the desired new sample names can not be matched simply by testing the identity at the start of both names.
| SampleName | ScientificName | OldSampleName |
|---|---|---|
| S10 | Staphylococcus aureus | Staaur-10 |
| S1 | Staphylococcus aureus | Staaur-1 |
In this case, the files Staaur-10_S10_L001_R1_001.fastq.gz and Staaur-10_S10_L001_R2_001.fastq.gz in the folder defined in link_directory will be matched to the sample name S10. Similarly, Staaur-1 will actually not match Staaur-10_S10_L001_R1_001.fastq.gz.
SRA samples¶
SRA samples will be determined based on the tabulated file whose full path must be passed to the variable sra_samples. The RunInfo files that can be downloaded through the SRA NCBI database can be directly passed without any modification. Otherwise, four columns must be defined.
| Run | SampleName | LibraryLayout | ScientificName |
|---|---|---|---|
| ERR1140788 | Mycobacterium_tuberculosis_N0145-Lineage_2 | paired | Mycobacterium tuberculosis |
| SRR006916 | Mycobacterium_tuberculosis_K21-Lineage_1 | single | Mycobacterium tuberculosis |