PathoFact issueshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues2021-01-12T15:25:57+01:00https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/40PlasFlow minimal contig length from config2021-01-12T15:25:57+01:00Valentina Galatavalentina.galata@uni.luPlasFlow minimal contig length from configGet the minimal contig length for `PlasFlow` from the config file: rule `filter_seq` in `Plasmid.smk`.Get the minimal contig length for `PlasFlow` from the config file: rule `filter_seq` in `Plasmid.smk`.Paper review - Microbiome - 1https://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/39Error if no VirSorter results in AMR_MGE.R2021-03-24T16:26:45+01:00Valentina Galatavalentina.galata@uni.luError if no VirSorter results in AMR_MGE.RIf `VirSorter` does not have any results then the script `AMR_MGE.R` fails with an error:
```
Error: `f` must be a factor (or character vector or numeric vector).
```
This happens here:
```R
Phage_prediction$VirSorter_prediction <- fct...If `VirSorter` does not have any results then the script `AMR_MGE.R` fails with an error:
```
Error: `f` must be a factor (or character vector or numeric vector).
```
This happens here:
```R
Phage_prediction$VirSorter_prediction <- fct_explicit_na(Phage_prediction$VirSorter_prediction, na_level = "-")
```
Reason: `Phage_prediction$VirSorter_prediction` contains only `NA`s.Paper review - Microbiome - 1Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://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/37PlasFlow threshold from config2021-01-12T15:25:03+01:00Valentina Galatavalentina.galata@uni.luPlasFlow threshold from configGet the parameter `threshold` for `PlasFlow` from the config file.Get the parameter `threshold` for `PlasFlow` from the config file.Paper review - Microbiome - 1Valentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/36README.md update2021-01-12T15:24:45+01:00Valentina Galatavalentina.galata@uni.luREADME.md update* [x] move "Pipeline environment" below "PathoFact"
- the env. can only be created after the repo has been cloned
* [x] remove `-b SpringClean` from the CMD for cloning the repo
* [x] in "Input files" there are two `SAMPLE_A.fna`: re...* [x] move "Pipeline environment" below "PathoFact"
- the env. can only be created after the repo has been cloned
* [x] remove `-b SpringClean` from the CMD for cloning the repo
* [x] in "Input files" there are two `SAMPLE_A.fna`: replace one with `SAMPLE_A.faa`Paper 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/34Replace SignalP2021-09-30T14:55:36+02:00Valentina Galatavalentina.galata@uni.luReplace SignalPReplace `SignalP` by a tool
- with same/better functionality
- more flexible license
- which can be installed automatically
- e.g. using `conda`, `git submodule` or by downloading a binary
Or, instead of using one tool, use a combin...Replace `SignalP` by a tool
- with same/better functionality
- more flexible license
- which can be installed automatically
- e.g. using `conda`, `git submodule` or by downloading a binary
Or, instead of using one tool, use a combination of several tools as it is done by [Uniprot](https://www.uniprot.org/help/signal)
*Add suggestions for tools as comments*Paper review - Microbiome - 1https://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/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/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/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/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/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 Denieshttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/26spring-clean: snakemake rules indentation2020-04-21T14:08:28+02:00Valentina Galatavalentina.galata@uni.luspring-clean: snakemake rules indentationFix formatting in all `snakemake` files (do **NOT** change the commands)
- Indentation: 4 spaces
Impact: Will not affect the pipelineFix formatting in all `snakemake` files (do **NOT** change the commands)
- Indentation: 4 spaces
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/25spring-clean: rm `configfile` from snakemake rule files2020-04-21T14:08:06+02:00Valentina Galatavalentina.galata@uni.luspring-clean: rm `configfile` from snakemake rule filesRemove `configfile` in all `snakemake` files except in `Snakemake`.
Otherwise it is impossible to use a custom file to call the pipeline.
Impact: Will not affect the pipelineRemove `configfile` in all `snakemake` files except in `Snakemake`.
Otherwise it is impossible to use a custom file to call the pipeline.
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/24spring-clean: add workflow parameter2020-04-21T13:47:28+02:00Valentina Galatavalentina.galata@uni.luspring-clean: add workflow parameter* [x] Add `workflow` variable to `config.yaml`
* [x] Adjust `Snakemake`* [x] Add `workflow` variable to `config.yaml`
* [x] Adjust `Snakemake`spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/23spring-clean: clean up YAML files2020-04-21T15:26:09+02:00Valentina Galatavalentina.galata@uni.luspring-clean: clean up YAML filesRemove `name` and `prefix` from `conda` YAML files, `conda` does not use them anyway.
Impact: Will not affect the pipelineRemove `name` and `prefix` from `conda` YAML files, `conda` does not use them anyway.
Impact: Will not affect the pipelinespring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/22spring-clean: HMMER2020-04-21T15:21:16+02:00Valentina Galatavalentina.galata@uni.luspring-clean: HMMERDependency: 'HMMER'
* [x] `conda` YAML file
* [x] update path in `config.yaml`
* [x] update rule(s)
Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore
- Confirm version: `3...Dependency: 'HMMER'
* [x] `conda` YAML file
* [x] update path in `config.yaml`
* [x] update rule(s)
Impact: Could affect the results if there are any discrepancies between the versions of any dependency. Therefore
- Confirm version: `3.2.1`spring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.luhttps://git-r3lab.uni.lu/laura.denies/PathoFact/-/issues/21spring-clean: VirSorter2020-04-21T15:10:53+02:00Valentina Galatavalentina.galata@uni.luspring-clean: VirSorterDependency: `VirSorter`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
Impact: Could affect the results if there are any discrepancies between the versions o...Dependency: `VirSorter`
* [x] `conda` YAML file
* [x] rm dir. in `scripts/`
* [x] rm `git clone` from `set-up.sh`
* [x] update path in `config.yaml`
Impact: Could affect the results if there are any discrepancies between the versions of any dependency.
Using `conda` installation (XX) instead of `git` repo (commit `v1.0.6-2-g52a1cd6`).
**NOTE**: [v1.0.6 vs. v1.0.6-2-g52a1cd6](https://github.com/simroux/VirSorter/compare/v1.0.6...v1.0.6-2-g52a1cd6)
--> **not sure** if all changes are non-criticalspring-cleanValentina Galatavalentina.galata@uni.luValentina Galatavalentina.galata@uni.lu