update functional_tests with new profiles

functional_tests/README.md

@@ -150,7 +150,7 @@ To use it :
   ``` 
   cut -f 1 $METAG_PATH/functional_tests/expected_processes_sr.tsv  | tail -n +2 > $OUTDIR/cmd_sr.sh
   ``` 
-  > the commands use profile `test_genotoul_workq`
+  > the commands use profile `test,genotoul`
   - replace path in the samplesheet : 
   ``` 
   sed -i -e "s,\$DATASET,$DATASET,g" $DATASET/small/input/samplesheet.csv

functional_tests/expected_processes_HiFi.tsv

 cmd	outputdir	DATABASES:INDEX_KAIJU	DATABASES:DOWNLOAD_TAXONOMY_DB	DATABASES:EGGNOG_MAPPER_DB	SH:S04_FILTERED_QUAST	SH:S04_STRUCTURAL_ANNOT:PROKKA	SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES	SH:S05_ALIGNMENT:DIAMOND	SH:S05_ALIGNMENT:MINIMAP2	SH:S06_FUNC_ANNOT:BEST_HITS	SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT	SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT	SH:S06_FUNC_ANNOT:EGGNOG_MAPPER	SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE	SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST	SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS	SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE	SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY	SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS
-mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7	$OUTDIR/hifi_all	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
-mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot	$OUTDIR/hifi_stop_at_structural_annot	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0
-mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .;  nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi	$OUTDIR/skip_func_annot-skip_taxo_affi	0	0	0	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
-mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .;  nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB`  --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd  --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot	$OUTDIR/skip_func_annot	0	0	0	1	1	1	1	1	0	0	0	0	0	0	0	0	1	1
-mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi	$OUTDIR/skip_taxo_affi	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0
+mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7	$OUTDIR/hifi_all	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
+mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot	$OUTDIR/hifi_stop_at_structural_annot	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0
+mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .;  nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi	$OUTDIR/skip_func_annot-skip_taxo_affi	0	0	0	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
+mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .;  nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB`  --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd  --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot	$OUTDIR/skip_func_annot	0	0	0	1	1	1	1	1	0	0	0	0	0	0	0	0	1	1
+mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi	$OUTDIR/skip_taxo_affi	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0

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 $METAG_PATH/main.nf --type 'SR' --input '$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"
+	--wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$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"