update docs + add environement variables

docs/usage.md

@@ -10,9 +10,9 @@
 
    > ```
    > sample,fastq_1,fastq_2
-   > a1,$DASTASET/a1_R1.fastq.gz,$DASTASET/a1_R2.fastq.gz
-   > a2,$DASTASET/a2_R1.fastq.gz,$DASTASET/a2_R2.fastq.gz
-   > c,$DASTASET/c_R1.fastq.gz,$DASTASET/c_R2.fastq.gz
+   > a1,$DATASET/a1_R1.fastq.gz,$DATASET/a1_R2.fastq.gz
+   > a2,$DATASET/a2_R1.fastq.gz,$DATASET/a2_R2.fastq.gz
+   > c,$DATASET/c_R1.fastq.gz,$DATASET/c_R2.fastq.gz
    > ```
 
 4. Run a basic script:
@@ -33,7 +33,7 @@
    > nextflow run -profile test_genotoul_workq metagwgs/main.nf \
    > --type 'SR' \
    > --input 'metagwgs-test-datasets/small/input/samplesheet.csv' \
-   > --skip_host_filter --skip_kaiju
+   > --skip_host_filter --skip_kaiju --stop_at_clean
    > ```
 
    > **NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3.

functional_tests/launch_example.sh

 #!/bin/bash
 
 sbatch -W -p workq -J functional_test --mem=6G \
-	--wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq main.nf --type 'SR' --input 'metagwgs-test-datasets/small/input/samplesheet.csv' --host_fasta 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir 'FT_banks_2021-10-19/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank 'FT_banks_2021-10-19/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir 'FT_banks_2021-10-19/eggnog-mapper-2.0.4-rf1/data' --taxonomy_dir 'FT_banks_2021-10-19/taxonomy_2021-08-23' --stop_at_clean -with-report -with-timeline -with-trace -with-dag"
\ No newline at end of file
+	--wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag"