Commit 4bfe5e51 authored by VIENNE MAINA's avatar VIENNE MAINA
Browse files

Update expected_processes_HiFi.tsv

parent 16ea1dd2
Pipeline #48159 skipped with stage
......@@ -2,5 +2,5 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGG
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_100000.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 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_100000.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 1 1
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_100000.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 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_100000.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 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_100000.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 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_100000.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 1 1
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