Commit b7bf5654 authored by Joanna Fourquet's avatar Joanna Fourquet
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Update use_case.md

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### D. Output files
With `Script_filtering_functional.sh` you have run all steps allowing to run `06_func_annot` step, including `03_filtering` step: `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot`, `05_alignment` and `06_func_annot`. But with the previous run script (`Script_filtering_binning.sh`) the steps `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot` and `05_alignment` have already been launched. This is why the jobs associated to these steps in the previous slurm file are indicated as "`cached`". Moreover, we keep `08_binning` and into `--step` parameter so the jobs associated to this step in the previous slurm file are also indicated as "`cached`". Keeping `06_func_annot` allows to have a new MultiQC report file updated with metrics of all steps launched in the two scripts. All output files of the pipeline related to these cached steps haven't been changed because they don't have been re-generated. They are presented into the chapter [IV.D](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md#d-output-files).
With `Script_filtering_functional.sh` you have run all steps allowing to run `06_func_annot` step, including `03_filtering` step: `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot`, `05_alignment` and `06_func_annot`. But with the previous run script (`Script_filtering_binning.sh`) the steps `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot` and `05_alignment` have already been launched. This is why the jobs associated to these steps in the previous slurm file are indicated as "`cached`". Moreover, we keep `08_binning` into `--step` parameter. The jobs related to this step have been already launched in the first script so they are also indicated as "`cached`". Keeping `06_func_annot` allows to have a new MultiQC report file updated with metrics of all steps launched in the two scripts. All output files of the pipeline related to these cached steps haven't been changed because they don't have been re-generated. They are presented into the chapter [IV.D](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md#d-output-files).
In the following sections, we will only present the main numerical output files in the subdirectory added to `results/` by this second script: `06_func_annot`.
#### 1. `06_func_annot/06_1_clustering`
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### D. Output files
With `Script_filtering_taxo.sh` you have run all steps allowing to run `07_taxo_affi` step, including `03_filtering` step: `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot`, `05_alignment` and `07_taxo_affi`. With the first script (`Script_filtering_binning.sh`) the steps `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot` and `05_alignment` have already been launched. This is why the jobs associated to these steps in the previous slurm file are indicated as "`cached`". Moreover, we keep `08_binning` and `06_func_annot` into `--step` parameter so the jobs associated to these steps in the previous slurm file are also indicated as "`cached`". Keeping `08_binning` and `06_func_annot` allows to have a new MultiQC report file updated with metrics of all steps launched in the three scripts. All output files of the pipeline related to these cached steps haven't been changed because they don't have been re-generated. They are presented into the chapters [IV.D](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md#d-output-files) and [V.D](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md#d-output-files-1).
With `Script_filtering_taxo.sh` you have run all steps allowing to run `07_taxo_affi` step, including `03_filtering` step: `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot`, `05_alignment` and `07_taxo_affi`. With the first script (`Script_filtering_binning.sh`) the steps `01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot` and `05_alignment` have already been launched. This is why the jobs associated to these steps in the previous slurm file are indicated as "`cached`". Moreover, we keep `08_binning` and `06_func_annot` into `--step` parameter. The jobs related to thess steps have been already launched in the first and in the second script so they are also indicated as "`cached`". Keeping `08_binning` and `06_func_annot` allows to have a new MultiQC report file updated with metrics of all steps launched in the three scripts. All output files of the pipeline related to these cached steps haven't been changed because they don't have been re-generated. They are presented into the chapters [IV.D](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md#d-output-files) and [V.D](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/use_case.md#d-output-files-1).
In the following sections, we will only present the main numerical output files in the subdirectory added to `results/` by this third script: `07_taxo_affi`.
#### 1. `07_taxo_affi/SAMPLE_NAME`
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