Commit 2c502b93 authored by Joanna Fourquet's avatar Joanna Fourquet
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Update usage.md

parent d6678cfe
......@@ -22,7 +22,7 @@
* Write in a file `Script.sh`:
> ```
> ```bash
> #!/bin/bash
> #SBATCH -p workq
> #SBATCH --mem=6G
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`Script.sh` is a basic script that requires only small test data input (available into [`metagwgs/test`](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/tree/dev/test)) and no other files. To analyze real data, in addition to your metagenomic whole genome shotgun `.fastq` files, you need to download different files which are described into the next chapter.
**WARNING:** if you run metagWGS to **analyze real metagenomics data on genologin cluster**, you have to use the `unlimitq` queue to run your Nextflow script: instead of writing in the second line of your script `#SBATCH -p workq` you need to write `#SBATCH -p unlimitq`.
> **WARNING:** if you run metagWGS to **analyze real metagenomics data on genologin cluster**, you have to use the `unlimitq` queue to run your Nextflow script: instead of writing in the second line of your script `#SBATCH -p workq` you need to write `#SBATCH -p unlimitq`.
## II. Input files
......@@ -142,12 +142,12 @@ The next parameters can be used when you run metagWGS.
`--step "your_step"`: indicate the step of the pipeline you want to run. The steps available are described in the [`README`](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/tree/dev#metagwgs-steps) (`01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot`, `05_alignment`, `06_func_annot`, `07_taxo_affi` and `08_binning`).
> **NOTES:**
i. You can directly indicate the final step that is important to you. For example, if you are interested in binning (and the taxonomic affiliation of bins), just use `--step "08_binning"`. It runs the previous steps automatically (except `03_filtering`, see ii).
**NOTES:**
**i. You can directly indicate the final step that is important to you. For example, if you are interested in binning (and the taxonomic affiliation of bins), just use `--step "08_binning"`. It runs the previous steps automatically (except `03_filtering`, see ii).**
ii. `03_filtering` is automatically skipped for the next steps `04_structural_annot`, `05_alignment`, `06_func_annot`, `07_taxo_affi` and `08_binning`. If you want to filter your assembly before doing one of these steps, you must use `--step "03_filtering,the_step"`, for example `--step "03_filtering,04_structural_annot"`.
**ii. `03_filtering` is automatically skipped for the next steps `04_structural_annot`, `05_alignment`, `06_func_annot`, `07_taxo_affi` and `08_binning`. If you want to filter your assembly before doing one of these steps, you must use `--step "03_filtering,the_step"`, for example `--step "03_filtering,04_structural_annot"`.**
iii. When you run one of the three steps `06_func_annot`, `07_taxo_affi` or `08_binning` during a first analysis and then another of these steps interests you and you run metagWGS again to get the result of this other step, you have to indicate `--step "the_first_step,the_second_step"`. This will allow you to have a final MultiQC html report that will take into account the metrics of both analyses performed. If the third of these steps interests you and you run again metagWGS for this step, you also have to indicate `--step "the_first_step,the_second_step,the_third,step"` for the same reasons.
**iii. When you run one of the three steps `06_func_annot`, `07_taxo_affi` or `08_binning` during a first analysis and then another of these steps interests you and you run metagWGS again to get the result of this other step, you have to indicate `--step "the_first_step,the_second_step"`. This will allow you to have a final MultiQC html report that will take into account the metrics of both analyses performed. If the third of these steps interests you and you run again metagWGS for this step, you also have to indicate `--step "the_first_step,the_second_step,the_third,step"` for the same reasons.**
When you want to run a particular step, you just need to specify its name:
......@@ -246,13 +246,14 @@ No parameters.
**WARNING 7:** `04_structural_annot` step depends on `01_clean_qc`, `02_assembly` and `03_filtering` (if you use it) steps. You need to use mandatory files of these four steps to run `04_structural_annot`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 6.
**WARNING 8:** if you haven't associated this step with `03_filtering`, calculation time of `04_structural_annot` can be important. Some cluster queues have defined calculation time, you need to adapt the queue you use to your data. For example, if you are on [genologin cluster](http://bioinfo.genotoul.fr/) and you haven't done `03_filtering` step, you can create into your working directory a file `nextflow.config` containing:
```bash
withName: prokka {
queue = 'unlimitq'
}
```
This will launch the `Prokka` command line of step `04_structural_annot` on a calculation queue (`unlimitq`) where the job can last more than 4 days (which is not the case for the usual `workq` queue).
**WARNING 8:** if you haven't associated this step with `03_filtering`, calculation time of `04_structural_annot` can be important. Some cluster queues have defined calculation time, you need to adapt the queue you use to your data.
> For example, if you are on [genologin cluster](http://bioinfo.genotoul.fr/) and you haven't done `03_filtering` step, you can create into your working directory a file `nextflow.config` containing:
> ```bash
> withName: prokka {
> queue = 'unlimitq'
> }
> ```
> This will launch the `Prokka` command line of step `04_structural_annot` on a calculation queue (`unlimitq`) where the job can last more than 4 days (which is not the case for the usual `workq` queue).
#### **`05_alignment` step:**
......@@ -304,6 +305,6 @@ See the description of output files in [this part](https://forgemia.inra.fr/geno
## VI. Analyze big test dataset with metagWGS in genologin cluster
If you have an account into [genologin cluster](http://bioinfo.genotoul.fr/) and you would like to familiarise yourself with metagWGS, see the tutorial available into the [use case documentation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md). It allows to analyze big test dataset with metagWGS.
> If you have an account into [genologin cluster](http://bioinfo.genotoul.fr/) and you would like to familiarise yourself with metagWGS, see the tutorial available into the [use case documentation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md). It allows to analyze big test dataset with metagWGS.
**WARNING:** the test dataset into `metagwgs/test` directory used in [I. Basic Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#i-basic-usage) is a small test dataset which does not allow to test all steps (`08_binning` doesn't work with this dataset).
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