Commit a689edb8 authored by VIENNE MAINA's avatar VIENNE MAINA
Browse files

update functional test to take into account new taxonomy parameters

parent 051b92ff
Pipeline #48007 skipped with stage
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 $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_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` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump $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_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 --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump –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
This diff is collapsed.
#!/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 $METAG_PATH/main.nf --type 'SR' --input '$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 '$EGGNOG_DB' --accession2taxid '$DATABANK/taxonomy_2021-12-7/prot.accession2taxid.FULL' --taxdump '$DATABANK/taxonomy_2021-12-7/new_taxdump' -with-report -with-timeline -with-trace -with-dag"
......@@ -7,7 +7,6 @@ process PROKKA {
output:
tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results
path "PROKKA_${sampleId}/${sampleId}.txt", emit: report
path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results
script:
"""
......
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