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
cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS
mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 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 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 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 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 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 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 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 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0
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