Commit e34af630 authored by VIENNE MAINA's avatar VIENNE MAINA
Browse files

correct host + taxonomy_dir paths

parent df0479a1
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_2021-08-23 $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_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_2021-08-23 –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_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
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