PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2020-04-21T15:53:04+02:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/28spring-clean: logging2020-04-21T15:53:04+02:00Valentina Galatavalentina.galata@uni.luspring-clean: logging- Add `log` to rules (if applicable)
- Add logging in R-scripts
```R
# logging in R scripts
sink(file=file(snakemake@log[[1]], open="wt"), type="message")
```
Impact: Will not affect the pipeline- Add `log` to rules (if applicable)
- Add logging in R-scripts
```R
# logging in R scripts
sink(file=file(snakemake@log[[1]], open="wt"), type="message")
```
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/15spring-clean: all scripts in scripts/2020-04-23T12:31:27+02:00Valentina Galatavalentina.galata@uni.luspring-clean: all scripts in scripts/* [x] mv scripts in `rules/` to `scripts/`
* [x] adjust paths when calling these scripts
Impact: Will not affect the pipeline* [x] mv scripts in `rules/` to `scripts/`
* [x] adjust paths when calling these scripts
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/31spring-clean: args in virulence_prediction.py and rule classifier in the vir ...2020-04-23T12:32:59+02:00Valentina Galatavalentina.galata@uni.luspring-clean: args in virulence_prediction.py and rule classifier in the vir stepScript `scripts/virulence_prediction.py` uses `snakemake` variable to access parameters but the rule `classfier` in `rules/Virulence/Virulence.snk` uses `shell` instead of `script`.Script `scripts/virulence_prediction.py` uses `snakemake` variable to access parameters but the rule `classfier` in `rules/Virulence/Virulence.snk` uses `shell` instead of `script`.spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/18spring-clean: give snakemake files an extension2020-04-24T10:43:37+02:00Valentina Galatavalentina.galata@uni.luspring-clean: give snakemake files an extensionAdd `.smk` to all `snakemake` files in `rules/` and `workflows/`.
Makes it easier to recognize `snakemake` files and to have code highlighting in editors.Add `.smk` to all `snakemake` files in `rules/` and `workflows/`.
Makes it easier to recognize `snakemake` files and to have code highlighting in editors.spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/30spring-clean: test data set2020-04-29T16:30:25+02:00Valentina Galatavalentina.galata@uni.luspring-clean: test data setAdd a test data set to be used to check whether the pipeline runs through and whether the results are consistent.
* [x] Create/copy input files (from `IMP3` test data set)
* [x] Create expected output (using `PathoFact`'s version of the...Add a test data set to be used to check whether the pipeline runs through and whether the results are consistent.
* [x] Create/copy input files (from `IMP3` test data set)
* [x] Create expected output (using `PathoFact`'s version of the `master` branch)
* [x] Create a config file
*Note: Scripts to compare the output will be part of a separate issue*spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/33spring-clean: add test workflow2020-04-30T08:04:55+02:00Valentina Galatavalentina.galata@uni.luspring-clean: add test workflowAdd a test workflow. Purpose:
- check whether the pipeline can be run
- check whether the pipeline produces the expected results
Tasks:
* [x] create a new `snakemake` file
* [x] create workflow
* [x] create rules
Impact: Will extend th...Add a test workflow. Purpose:
- check whether the pipeline can be run
- check whether the pipeline produces the expected results
Tasks:
* [x] create a new `snakemake` file
* [x] create workflow
* [x] create rules
Impact: Will extend the pipeline, old workflows will remain untouchedspring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/32spring-clean: escape special chars in rules properly2020-04-30T08:05:22+02:00Valentina Galatavalentina.galata@uni.luspring-clean: escape special chars in rules properlyEscape special chars in rules' shell call properly, e.g. replace `\t` by `\\t`.
Reason: Prevents `snakemake` from interpreting these characters.
Impact: Should not affect the pipelineEscape special chars in rules' shell call properly, e.g. replace `\t` by `\\t`.
Reason: Prevents `snakemake` from interpreting these characters.
Impact: Should not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/29spring-clean: snakemake rules: use names in shell/run/script2020-04-30T09:08:33+02:00Valentina Galatavalentina.galata@uni.luspring-clean: snakemake rules: use names in shell/run/scriptWhen accessing `snakemake` variables use names if provided, e.g. `snakemake@input[["faa"]]` in an `R` script.
Impact: Will not affect the pipelineWhen accessing `snakemake` variables use names if provided, e.g. `snakemake@input[["faa"]]` in an `R` script.
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/9IMPiris: test data2020-05-05T07:19:06+02:00Valentina Galatavalentina.galata@uni.luIMPiris: test dataCreate a test data setCreate a test data setValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/7IMPiris: log files2020-05-05T07:19:17+02:00Valentina Galatavalentina.galata@uni.luIMPiris: log filesAdd `log` files to rules
* [x] redirect for CMD
* [ ] logging in scripts
* [x] R scripts
* [ ] Python scriptsAdd `log` files to rules
* [x] redirect for CMD
* [ ] logging in scripts
* [x] R scripts
* [ ] Python scriptsValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/49Replace SeqKit2020-06-11T15:38:12+02:00Valentina Galatavalentina.galata@uni.luReplace SeqKitReviewers reported issues with `SeqKit`.
Since it is used for FASTA splitting it can be replaced easily.Reviewers reported issues with `SeqKit`.
Since it is used for FASTA splitting it can be replaced easily.Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/50Add Prodigal to Pipeline2020-06-11T15:38:23+02:00Laura DeniesAdd Prodigal to PipelineLaura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/38size_fasta is not used by seqkit2020-06-11T15:40:51+02:00Valentina Galatavalentina.galata@uni.lusize_fasta is not used by seqkitThe parameter `size_fasta` from the config file is not used in any of the rules.
All `seqkit split2` calls contain `-s 10000`The parameter `size_fasta` from the config file is not used in any of the rules.
All `seqkit split2` calls contain `-s 10000`Paper review - Microbiome - 1Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/43Add RGI (AMR prediction)2020-06-18T13:23:04+02:00Valentina Galatavalentina.galata@uni.luAdd RGI (AMR prediction)Add `RGI` for AMR prediction
- [paper](https://pubmed.ncbi.nlm.nih.gov/31665441/)
- [repo](https://github.com/arpcard/rgi)
* [x] Evaluate for incorporation
* [x] `conda` YAML file
* [x] relevant parameters in config
* [x] rule to gener...Add `RGI` for AMR prediction
- [paper](https://pubmed.ncbi.nlm.nih.gov/31665441/)
- [repo](https://github.com/arpcard/rgi)
* [x] Evaluate for incorporation
* [x] `conda` YAML file
* [x] relevant parameters in config
* [x] rule to generate predictions
* [x] combine with other resultsPaper review - Microbiome - 1Laura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/51Update deeparg installation2020-06-18T16:58:08+02:00Laura DeniesUpdate deeparg installationInclude upgraded installation method of deepargInclude upgraded installation method of deeparghttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/44DeepARG - parameters in config file2020-06-22T11:26:03+02:00Valentina Galatavalentina.galata@uni.luDeepARG - parameters in config fileAdd relevant parameters to config fileAdd relevant parameters to config filePaper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/35Update SignalP2020-06-22T11:26:19+02:00Valentina Galatavalentina.galata@uni.luUpdate SignalPConsider using version `5.0b` instead of `4.X`.
See the list of available versions [here](https://services.healthtech.dtu.dk/software.php).
Related to issue #34: no need for an update if `SignalP` will be replaced by a different tool.Consider using version `5.0b` instead of `4.X`.
See the list of available versions [here](https://services.healthtech.dtu.dk/software.php).
Related to issue #34: no need for an update if `SignalP` will be replaced by a different tool.Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/48Output format2020-06-22T13:37:43+02:00Valentina Galatavalentina.galata@uni.luOutput formatUse consistent output format
* [x] Either `TSV` or `CSV`, not both
* [x] Labels: `pathogenic`, `non-pathogenic` etc.Use consistent output format
* [x] Either `TSV` or `CSV`, not both
* [x] Labels: `pathogenic`, `non-pathogenic` etc.Paper review - Microbiome - 1Laura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/45Reduce output size2020-06-22T14:40:26+02:00Valentina Galatavalentina.galata@uni.luReduce output sizeRemove all intermediate files which are not relevant to the user.
Files with relevant results should be compressed, e.g. output created by `PlasFlow`.
Check if there are very large log files.
* [x] make not relevant intermediate files t...Remove all intermediate files which are not relevant to the user.
Files with relevant results should be compressed, e.g. output created by `PlasFlow`.
Check if there are very large log files.
* [x] make not relevant intermediate files temporary w/ `temp(...)`
* [ ] redirect `hmmer`s stdout to `/dev/null` instead of the log file
* [ ] compress relevant intermediate files
* [x] add rule to removes files which cannot be made temp() (files used in snakemake checkpoints) Paper review - Microbiome - 1Laura DeniesLaura Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/27Snakemake rule messages2020-08-06T12:06:37+02:00Valentina Galatavalentina.galata@uni.luSnakemake rule messagesAdd a short message to each `snakemake` rule
Impact: Will not affect the pipelineAdd a short message to each `snakemake` rule
Impact: Will not affect the pipelinePaper review - Microbiome - 1Laura DeniesLaura Denies