Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
genotoul-bioinfo
metagWGS
Commits
c95e3a73
Commit
c95e3a73
authored
Jan 10, 2022
by
VIENNE MAINA
Browse files
correct host + taxonomy_dir paths
parent
0fa08f53
Changes
2
Expand all
Hide whitespace changes
Inline
Side-by-side
functional_tests/expected_processes_HiFi.tsv
View file @
c95e3a73
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
functional_tests/expected_processes_sr.tsv
View file @
c95e3a73
This diff is collapsed.
Click to expand it.
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment