Commit 828d606b authored by VIENNE MAINA's avatar VIENNE MAINA
Browse files

update docs + add environement variables

parent 96471aed
...@@ -10,9 +10,9 @@ ...@@ -10,9 +10,9 @@
> ``` > ```
> sample,fastq_1,fastq_2 > sample,fastq_1,fastq_2
> a1,$DASTASET/a1_R1.fastq.gz,$DASTASET/a1_R2.fastq.gz > a1,$DATASET/a1_R1.fastq.gz,$DATASET/a1_R2.fastq.gz
> a2,$DASTASET/a2_R1.fastq.gz,$DASTASET/a2_R2.fastq.gz > a2,$DATASET/a2_R1.fastq.gz,$DATASET/a2_R2.fastq.gz
> c,$DASTASET/c_R1.fastq.gz,$DASTASET/c_R2.fastq.gz > c,$DATASET/c_R1.fastq.gz,$DATASET/c_R2.fastq.gz
> ``` > ```
4. Run a basic script: 4. Run a basic script:
...@@ -33,7 +33,7 @@ ...@@ -33,7 +33,7 @@
> nextflow run -profile test_genotoul_workq metagwgs/main.nf \ > nextflow run -profile test_genotoul_workq metagwgs/main.nf \
> --type 'SR' \ > --type 'SR' \
> --input 'metagwgs-test-datasets/small/input/samplesheet.csv' \ > --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. > **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.
......
#!/bin/bash #!/bin/bash
sbatch -W -p workq -J functional_test --mem=6G \ 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" --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"
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