changes to doc

docs/installation.md

@@ -32,7 +32,7 @@ A directory called `metagwgs` containing all source files of the pipeline have b
 
 ## III. Install Singularity
 
-metagWGS needs two [Singularity](https://sylabs.io/docs/) containers to run: Singularity version 3 or above must be installed.
+metagWGS needs three [Singularity](https://sylabs.io/docs/) containers to run: Singularity version 3 or above must be installed.
 
 See [here](https://sylabs.io/guides/3.7/user-guide/quick_start.html#quick-installation-steps) how to install Singularity >=v3.
 
@@ -43,9 +43,9 @@ See [here](https://sylabs.io/guides/3.7/user-guide/quick_start.html#quick-instal
 
 ## IV. Download or build Singularity containers
 
-You can directly download the two Singularity containers (`Solution 1`, recommended) or build them (`Solution 2`).
+You can directly download the three Singularity containers (`Solution 1`, recommended) or build them (`Solution 2`).
 
-### Solution 1 (recommended): download the two containers
+### Solution 1 (recommended): download the three containers
 
 **In the directory you want tu run the workflow**, where you have the directory `metagwgs` with metagWGS source files, run these command lines:
 
@@ -53,22 +53,26 @@ You can directly download the two Singularity containers (`Solution 1`, recommen
 cd metagwgs/env/
 singularity pull eggnog_mapper.sif oras://registry.forgemia.inra.fr/genotoul-bioinfo/metagwgs/eggnog_mapper:latest
 singularity pull metagwgs.sif oras://registry.forgemia.inra.fr/genotoul-bioinfo/metagwgs/metagwgs:latest
+singularity pull mosdepth.sif oras://registry.forgemia.inra.fr/genotoul-bioinfo/metagwgs/metagwgs:latest
 ```
 
-Two files (`metagwgs.sif` and `eggnog_mapper.sif`) must have been downloaded.
+Three files (`metagwgs.sif`, `eggnog_mapper.sif` and `mosdepth.sif`) must have been downloaded.
 
-### Solution 2: build the two containers.
+### Solution 2: build the three containers.
 
-**In the directory you want tu run the workflow**, where you have downloaded metagWGS source files, go to `metagwgs/env/` directory, and follow [these explanations](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/wikis/Singularity%20container) to build the two containers. You need two files by container to build them. These files are into the `metagwgs/env/` folder and you can read them here:
+**In the directory you want tu run the workflow**, where you have downloaded metagWGS source files, go to `metagwgs/env/` directory, and follow [these explanations](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/wikis/Singularity%20container) to build the three containers. You need three files by container to build them. These files are into the `metagwgs/env/` folder and you can read them here:
 
 * metagwgs.sif container
    * [metagWGS recipe file](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/Singularity_recipe_metagWGS)
    * [metagWGS.yml](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/metagWGS.yml)
-* eggnog_mapper container
+* eggnog_mapper.sif container
    * [eggnog_mapper recipe file](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/Singularity_recipe_eggnog_mapper)
    * [eggnog_mapper.yml](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/eggnog_mapper.yml)
+* mosdepth.sif container
+   * [mosdepth recipe file] https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/Singularity_recipe_mosdepth
+   * [mosdepth.yml] https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/env/mosdepth.yml
 
-At the end of the build, two files (`metagwgs.sif` and `eggnog_mapper.sif`) must have been generated.
+At the end of the build, three files (`metagwgs.sif`, `eggnog_mapper.sif` and `mosdepth.sif`) must have been generated.
 
 ## V. Use metagWGS
 

docs/usage.md

@@ -223,7 +223,7 @@ No parameter available for this substep.
 
 * `--kaiju_db_dir "PATH/directory"`: if you have already downloaded the kaiju database, indicate its directory. **WARNING:** you will not be able to use kaiju database built with `kaiju-makedb` command line. Default: `--kaiju_db_dir false`. See **WARNING 2**.
 
-* `--kaiju_db "http://kaiju.binf.ku.dk/database/CHOOSEN_DATABASE.tgz"`: allows metagWGS to download kaiju database of your choice. The list of kaiju databases is available in [kaiju website](http://kaiju.binf.ku.dk/server), in the blue insert on the left side. Default: `--kaiju_db false`. See **WARNING 2**.
+* `--kaiju_db "http://kaiju.binf.ku.dk/database/CHOOSEN_DATABASE.tgz"`: allows metagWGS to download kaiju database of your choice. The list of kaiju databases is available in [kaiju website](http://kaiju.binf.ku.dk/server), in the blue insert on the left side. Default: `--kaiju_db https://kaiju.binf.ku.dk/database/kaiju_db_refseq_2021-02-26.tgz`. See **WARNING 2**.
 
 * `--skip_kaiju`: allows to skip taxonomic affiliation of reads with kaiju. Krona files will not be generated. Use: `--skip_kaiju`. See **WARNING 2**.
 
@@ -288,6 +288,8 @@ No parameters.
 
 * `--taxdump "FTP_PATH_TO_taxdump.tar.gz"`: indicates the FTP adress of the NCBI file `taxdump.tar.gz`. Default `"ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"`.
 
+* `--taxonomy_dir "PATH/directory": if you have already downloaded the accession2taxid and taxdump databases, indicate their parent directory. Default: `--taxonomy_dir false`.`
+
 #### **`08_binning` step:**
 
 **WARNING 13:** `08_binning` step depends on `01_clean_qc`, `02_assembly`, `03_filtering` (if you use it), `04_structural_annot` and `05_alignment` steps. You need to use mandatory files of these six steps to run `08_binning`. See [II. Input files](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/usage.md#ii-input-files) and WARNINGS from 1 to 9.

functional_tests/main.py

@@ -8,7 +8,7 @@
 
 # Usage
     ## cd [work_directory]
-    ## python metagwgs/functional_tests/main.py -step [step] -exp_dir ./test_expected_logs -obs_dir ./[work_directory]/results [optional: --script ./[work_directory]/launch_nextflow.sh]
+    ## python metagwgs/functional_tests/main.py -step [step] -exp_dir ./test_expected_logs -obs_dir ./[work_directory]/results [optional: --script ./[work_directory]/launch_nextflow.sh] [optional: --verbose]
 
 try:
     import sys