update docs after merge

docs/installation.md

@@ -71,20 +71,6 @@ two files (`metagwgs.sif` and `eggnog_mapper.sif`) must have been downloaded.
 At the end of the build, two files (`metagwgs.sif` and `eggnog_mapper.sif`) must have been generated.
 
 
-**WARNING:** to ensure Nextflow can find the _.sif_ files, we encourage you to change the _nextflow.config_ file in metagWGS to contain these lines:
-```
-process {
-    container = '<PATH>/metagwgs.sif'
-    withLabel: eggnog {
-        container = '<PATH>/eggnog_mapper.sif'
-    }
-    withLabel: mosdepth {
-        container = '<PATH>/mosdepth.sif'
-    }
-}
-```
-Where \<PATH\> leads to the directory where the singularity images are built/downloaded.
-
 ## V. Use metagWGS
 
 See the [Usage](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/master/docs/usage.md) documentation to know how to run metagWGS.

functional_tests/README.md

@@ -62,9 +62,9 @@ python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET
 
 ## III. Output
 
-A `ft_[STEP].log` file is created for each step of metagwgs. It contains information about each test performed on given files.
+A ft_\[step\].log file is created for each step of metagwgs. It contains information about each test performed on given files.
 
-Exemple with `ft_01_clean_qc.log`:
+Exemple with ft_01_clean_qc.log:
 
 ```
 Expected directory: metagwgs-test-datasets/output/01_clean_qc
@@ -103,7 +103,7 @@ Not tested: 0
 
 If a test resulted in 'Failed' instead of 'Passed', the stdout is printed in log.
 
-Sometimes, files are not tested because present in _exp_dir_ but not in _obs_dir_. Then a log `ft_[STEP].not_tested` is created containing names of missing files. In **02_assembly**, there are two possible assembly programs that can be used: _metaspades_ and _megahit_, resulting in this `.not_tested log` file. Not tested files are not counted in missed count.
+Sometimes, files are not tested because present in exp_dir but not in obs_dir. Then a log ft_\[step\].not_tested is created containing names of missing files. In 02_assembly, there are two possible assembly programs that can be used: metaspades and megahit, resulting in this .not_tested log file. Not tested files are not counted in missed count.
 
 
 ### Test methods
@@ -113,23 +113,14 @@ Sometimes, files are not tested because present in _exp_dir_ but not in _obs_dir
 sort_diff: simple bash difference between two files
 `diff <(sort exp_path) <(sort obs_path)`
 
-- **diff**: simple bash difference between two files
-    
-    `diff exp_path obs_path`
-
-- **zdiff**: simple bash difference between two gzipped files
-
-    `zdiff exp_path obs_path`
-
-- **no_header_diff**: remove the headers of .annotations and .seed_orthologs files
-
-    `diff <(grep -w "^?#" exp_path) <(grep -w "^?#" obs_path)`
-
-- **cut_diff**: exception for cutadapt.log file
+zdiff: simple bash difference between two gzipped files
+`zdiff exp_path obs_path`
 
-    `diff <(tail -n+6 exp_path) <(tail -n+6 obs_path)`
+no_header_diff: remove the headers of .annotations and .seed_orthologs files
+`diff <(grep -w "^?#" exp_path) <(grep -w "^?#" obs_path)`
 
-- **not_empty**: in python, check if file is empty
+cut_diff: exception for cutadapt.log file
+`diff <(tail -n+6 exp_path) <(tail -n+6 obs_path)`
 
 not_empty: in python, check if file is empty
 `test = path.getsize(obs_path) > 0`