LICENSE
MANIFEST.in
README.md
environment.yml
pyproject.toml
requirements.txt
buisciii/__init__.py
buisciii/__main__.py
buisciii/archive.py
buisciii/autoclean_sftp.py
buisciii/bioinfo_doc.py
buisciii/clean.py
buisciii/config_json.py
buisciii/copy_sftp.py
buisciii/drylab_api.py
buisciii/list.py
buisciii/new_service.py
buisciii/scratch.py
buisciii/service_json.py
buisciii/utils.py
buisciii/assets/BU_ISCIII_logo.png
buisciii/assets/css/bootstrap.min.css
buisciii/assets/reports/md/assembly.md
buisciii/assets/reports/md/irma.md
buisciii/assets/reports/md/pikavirus.md
buisciii/assets/reports/md/plasmidid.md
buisciii/assets/reports/md/rnaseq_deg.md
buisciii/assets/reports/md/sarek.md
buisciii/assets/reports/md/taxprofiler.md
buisciii/assets/reports/md/viralrecon.md
buisciii/assets/reports/md/wgmlst_chewbbaca.md
buisciii/assets/reports/md/images/ALM-ASM.png
buisciii/assets/reports/md/images/IRMA_workflow.png
buisciii/assets/reports/md/images/KPN30_000240185_summary.png
buisciii/assets/reports/md/images/NIPH-NIPHEM.png
buisciii/assets/reports/md/images/PLOT.png
buisciii/assets/reports/md/images/SEN30_000195995_NC_013365.1.png
buisciii/assets/reports/md/images/asciigenome_screenshot.png
buisciii/assets/reports/md/images/deseq2_boxplot.png
buisciii/assets/reports/md/images/deseq2_cluster_dendogram.png
buisciii/assets/reports/md/images/deseq2_dispersion-estimate.png
buisciii/assets/reports/md/images/deseq2_heatmap-top-20-genes.png
buisciii/assets/reports/md/images/deseq2_heatmap_all.png
buisciii/assets/reports/md/images/deseq2_maplot.png
buisciii/assets/reports/md/images/deseq2_pca.png
buisciii/assets/reports/md/images/deseq2_plotSD.png
buisciii/assets/reports/md/images/deseq2_pvalue-hist.png
buisciii/assets/reports/md/images/deseq2_qc_plots.png
buisciii/assets/reports/md/images/deseq2_sample-to-sample.png
buisciii/assets/reports/md/images/dupradar_example_plot.png
buisciii/assets/reports/md/images/exomiser-html-description-1.png
buisciii/assets/reports/md/images/exomiser-html-description-2.png
buisciii/assets/reports/md/images/fastqc.png
buisciii/assets/reports/md/images/icarus.png
buisciii/assets/reports/md/images/kraken2.png
buisciii/assets/reports/md/images/mag_logo.png
buisciii/assets/reports/md/images/mag_logo.svg
buisciii/assets/reports/md/images/mag_workflow.png
buisciii/assets/reports/md/images/mag_workflow.svg
buisciii/assets/reports/md/images/mqc_alignment_check.png
buisciii/assets/reports/md/images/mqc_bcftools_stats_plot.png
buisciii/assets/reports/md/images/mqc_bowtie2_plot.png
buisciii/assets/reports/md/images/mqc_cutadapt_plot.png
buisciii/assets/reports/md/images/mqc_cutadapt_trimmed.png
buisciii/assets/reports/md/images/mqc_deseq2_clustering.png
buisciii/assets/reports/md/images/mqc_deseq2_pca.png
buisciii/assets/reports/md/images/mqc_dupradar.png
buisciii/assets/reports/md/images/mqc_fastp_plot.png
buisciii/assets/reports/md/images/mqc_fastqc_adapter.png
buisciii/assets/reports/md/images/mqc_fastqc_counts.png
buisciii/assets/reports/md/images/mqc_fastqc_plot.png
buisciii/assets/reports/md/images/mqc_fastqc_quality.png
buisciii/assets/reports/md/images/mqc_featurecounts_biotype.png
buisciii/assets/reports/md/images/mqc_hisat2.png
buisciii/assets/reports/md/images/mqc_ivar_trim_plot.png
buisciii/assets/reports/md/images/mqc_ivar_variants_plot.png
buisciii/assets/reports/md/images/mqc_kraken2_plot.png
buisciii/assets/reports/md/images/mqc_mosdepth_plot.png
buisciii/assets/reports/md/images/mqc_picard_duplicates_plot.png
buisciii/assets/reports/md/images/mqc_picard_insert_size_plot.png
buisciii/assets/reports/md/images/mqc_picard_markduplicates.png
buisciii/assets/reports/md/images/mqc_preseq_plot.png
buisciii/assets/reports/md/images/mqc_qualimap_coverage.png
buisciii/assets/reports/md/images/mqc_qualimap_features.png
buisciii/assets/reports/md/images/mqc_quast_plot.png
buisciii/assets/reports/md/images/mqc_rsem_mapped.png
buisciii/assets/reports/md/images/mqc_rsem_multimapped.png
buisciii/assets/reports/md/images/mqc_rseqc_inferexperiment.png
buisciii/assets/reports/md/images/mqc_rseqc_innerdistance.png
buisciii/assets/reports/md/images/mqc_rseqc_junctionannotation.png
buisciii/assets/reports/md/images/mqc_rseqc_junctionsaturation.png
buisciii/assets/reports/md/images/mqc_rseqc_readdistribution.png
buisciii/assets/reports/md/images/mqc_rseqc_readduplication.png
buisciii/assets/reports/md/images/mqc_salmon.png
buisciii/assets/reports/md/images/mqc_samtools_idxstats.png
buisciii/assets/reports/md/images/mqc_samtools_mapped.png
buisciii/assets/reports/md/images/mqc_samtools_stats_plot.png
buisciii/assets/reports/md/images/mqc_snpeff_plot.png
buisciii/assets/reports/md/images/mqc_sortmerna.png
buisciii/assets/reports/md/images/mqc_star.png
buisciii/assets/reports/md/images/mqc_strand_check.png
buisciii/assets/reports/md/images/mqc_varscan2_plot.png
buisciii/assets/reports/md/images/nanoplot.png
buisciii/assets/reports/md/images/nanoplot_readlengthquality.png
buisciii/assets/reports/md/images/nextclade_tag_example.png
buisciii/assets/reports/md/images/nf-core-mag_logo.png
buisciii/assets/reports/md/images/nf-core-mag_logo_dark.png
buisciii/assets/reports/md/images/nf-core-mag_logo_light.png
buisciii/assets/reports/md/images/nf-core-rnaseq_metro_map_grey.png
buisciii/assets/reports/md/images/nf-core-viralrecon_logo_dark.png
buisciii/assets/reports/md/images/nf-core-viralrecon_logo_light.png
buisciii/assets/reports/md/images/nf-core-viralrecon_metro_map.svg
buisciii/assets/reports/md/images/nf-core-viralrecon_metro_map_illumina.png
buisciii/assets/reports/md/images/nf-core-viralrecon_metro_map_nanopore.png
buisciii/assets/reports/md/images/prokka.png
buisciii/assets/reports/md/images/pycoqc_readsperbarcode.png
buisciii/assets/reports/md/images/quast.png
buisciii/assets/reports/md/images/r_amplicon_barplot.png
buisciii/assets/reports/md/images/r_amplicon_heatmap.png
buisciii/assets/reports/md/images/r_genome_coverage.png
buisciii/assets/reports/results/assembly.md
buisciii/assets/reports/results/exomeeb.md
buisciii/assets/reports/results/irma_output.md
buisciii/assets/reports/results/pikavirus.md
buisciii/assets/reports/results/plasmidid.md
buisciii/assets/reports/results/rnaseq_deg.md
buisciii/assets/reports/results/taxprofiler.md
buisciii/assets/reports/results/trios.md
buisciii/assets/reports/results/viralrecon.md
buisciii/assets/reports/results/wgmlst_chewbbaca.md
buisciii/conf/configuration.json
buisciii/conf/configuration_dev.json
buisciii/schemas/deliver_automatization.json
buisciii/templates/email.j2
buisciii/templates/html_service_template.html
buisciii/templates/jinja_template_delivery.j2
buisciii/templates/jinja_template_service_info.j2
buisciii/templates/services.json
buisciii/templates/sftp_user.json
buisciii/templates/IRMA/ANALYSIS/lablog_irma
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/lablog
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/01-preproQC/lablog
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/02-preprocessing/lablog
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/03-procQC/lablog
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/create_irma_stats_flu.sh
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/create_irma_stats_rsv.sh
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/create_irma_vcf.py
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/lablog_flu
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/lablog_rsv
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/postprocessing_flu.sh
buisciii/templates/IRMA/ANALYSIS/ANALYSIS01_IRMA/04-irma/postprocessing_rsv.sh
buisciii/templates/IRMA/DOC/irma_config.sh
buisciii/templates/IRMA/RAW/README
buisciii/templates/IRMA/REFERENCES/README
buisciii/templates/IRMA/RESULTS/lablog_irma_results
buisciii/templates/IRMA/TMP/README
buisciii/templates/assembly/ANALYSIS/lablog_assembly
buisciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog
buisciii/templates/assembly/DOC/hpc_slurm_assembly.config
buisciii/templates/assembly/RAW/README
buisciii/templates/assembly/REFERENCES/README
buisciii/templates/assembly/RESULTS/README
buisciii/templates/assembly/RESULTS/lablog_assembly_results
buisciii/templates/assembly/TMP/README
buisciii/templates/blast_nt/ANALYSIS/lablog_blast_nt
buisciii/templates/blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog
buisciii/templates/blast_nt/DOC/README
buisciii/templates/blast_nt/RAW/README
buisciii/templates/blast_nt/REFERENCES/README
buisciii/templates/blast_nt/RESULTS/README
buisciii/templates/blast_nt/TMP/README
buisciii/templates/characterization/ANALYSIS/lablog_characterization
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/01-preprocessing/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/03-amrfinderplus/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/05-mlva/lablog
buisciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/99-stats/lablog
buisciii/templates/characterization/DOC/README
buisciii/templates/characterization/RAW/README
buisciii/templates/characterization/REFERENCES/README
buisciii/templates/characterization/REFERENCES/lablog_pubmlst
buisciii/templates/characterization/RESULTS/lablog_characterization_results
buisciii/templates/characterization/TMP/README
buisciii/templates/chewbbaca/ANALYSIS/lablog_chewbbaca
buisciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/lablog
buisciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog
buisciii/templates/chewbbaca/DOC/README
buisciii/templates/chewbbaca/RAW/README
buisciii/templates/chewbbaca/REFERENCES/README
buisciii/templates/chewbbaca/REFERENCES/lablog_chewbbaca
buisciii/templates/chewbbaca/RESULTS/lablog_mlst_results
buisciii/templates/chewbbaca/TMP/README
buisciii/templates/exomeeb/ANALYSIS/lablog_exomeeb
buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog
buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog
buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/exomiser_configfile.yml
buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog
buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/merge_dbNSFP.R
buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/merge_parse.R
buisciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog
buisciii/templates/exomeeb/DOC/hpc_slurm_sarek.config
buisciii/templates/exomeeb/RAW/README
buisciii/templates/exomeeb/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2.txt
buisciii/templates/exomeeb/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.bed
buisciii/templates/exomeeb/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list
buisciii/templates/exomeeb/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37_mod.bed
buisciii/templates/exomeeb/REFERENCES/README
buisciii/templates/exomeeb/RESULTS/README
buisciii/templates/exomeeb/RESULTS/lablog_exomeeb_results
buisciii/templates/exomeeb/TMP/README
buisciii/templates/exometrio/ANALYSIS/lablog
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/Merge_All.R
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/exomiser_configfile.yml
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/header_vep_final_annot.txt
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/inheritance_types.txt
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog
buisciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog
buisciii/templates/exometrio/DOC/hpc_slurm_sarek.config
buisciii/templates/exometrio/RAW/Illumine_Exome_CEX_TargetedRegions_v1.2.txt
buisciii/templates/exometrio/RAW/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.bed
buisciii/templates/exometrio/RAW/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list
buisciii/templates/exometrio/RAW/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37_mod.bed
buisciii/templates/exometrio/RAW/README
buisciii/templates/exometrio/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2.txt
buisciii/templates/exometrio/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.bed
buisciii/templates/exometrio/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list
buisciii/templates/exometrio/REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37_mod.bed
buisciii/templates/exometrio/REFERENCES/README
buisciii/templates/exometrio/RESULTS/lablog_exome_results
buisciii/templates/exometrio/TMP/README
buisciii/templates/freebayes_outbreak/ANALYSIS/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/01-preproQC/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/02-preprocessing/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/03-procQC/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/04-Alignment/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/05-mark_dups/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/06-freebayes/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/07-snphylo/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/08-iqtree/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/99-stats/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/lablog
buisciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/multiqc_config.yaml
buisciii/templates/freebayes_outbreak/DOC/mag.config
buisciii/templates/lowfreq_panel/ANALYSIS/lablog_lowfreqpanel
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/01-fastQC/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/02-preprocessing/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/03-preprocQC/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/04-mapping/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/05-samtools/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/06-VarScan/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/header
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/merge_parse.R
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/lablog
buisciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/multiqc_config.yaml
buisciii/templates/lowfreq_panel/DOC/README
buisciii/templates/lowfreq_panel/RAW/README
buisciii/templates/lowfreq_panel/REFERENCES/README
buisciii/templates/lowfreq_panel/REFERENCES/designed-probe-coords.bed
buisciii/templates/lowfreq_panel/REFERENCES/header
buisciii/templates/lowfreq_panel/REFERENCES/idt_rb1_panel_20221123.bed
buisciii/templates/lowfreq_panel/REFERENCES/idt_rb1_panel_20221123.interval_list
buisciii/templates/lowfreq_panel/REFERENCES/idt_rb1_panel_20221123_probes.bed
buisciii/templates/lowfreq_panel/REFERENCES/idt_rb1_panel_20221123_probes.interval_list
buisciii/templates/lowfreq_panel/REFERENCES/my-targets.bed
buisciii/templates/lowfreq_panel/RESULTS/README
buisciii/templates/lowfreq_panel/RESULTS/lablog_lowfreq_panel_results
buisciii/templates/lowfreq_panel/TMP/README
buisciii/templates/mtbseq/ANALYSIS/lablog_mtbseq
buisciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/lablog
buisciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/01-preprocessing/lablog
buisciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/02-kmerfinder/lablog
buisciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/03-MTBSeq/lablog
buisciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/03-MTBSeq/all_samples/lablog
buisciii/templates/mtbseq/DOC/README
buisciii/templates/mtbseq/RAW/README
buisciii/templates/mtbseq/REFERENCES/README
buisciii/templates/mtbseq/RESULTS/README
buisciii/templates/mtbseq/RESULTS/lablog_mtbseq_results
buisciii/templates/mtbseq/TMP/README
buisciii/templates/pikavirus/ANALYSIS/lablog_pikavirus
buisciii/templates/pikavirus/ANALYSIS/ANALYSIS01_PIKAVIRUS/lablog
buisciii/templates/pikavirus/DOC/hpc_slurm_pikavirus.config
buisciii/templates/pikavirus/RAW/README
buisciii/templates/pikavirus/REFERENCES/README
buisciii/templates/pikavirus/RESULTS/README
buisciii/templates/pikavirus/TMP/README
buisciii/templates/plasmidid/ANALYSIS/lablog_plasmidid
buisciii/templates/plasmidid/ANALYSIS/ANALYSIS02_PLASMIDID/lablog
buisciii/templates/plasmidid/ANALYSIS/ANALYSIS02_PLASMIDID/plasmidID_annotation_config_file.txt
buisciii/templates/plasmidid/DOC/README
buisciii/templates/plasmidid/RAW/README
buisciii/templates/plasmidid/REFERENCES/README
buisciii/templates/plasmidid/RESULTS/README
buisciii/templates/plasmidid/RESULTS/lablog_plasmidid_results
buisciii/templates/plasmidid/TMP/README
buisciii/templates/rnaseq/ANALYSIS/lablog_rnaseq
buisciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/lablog
buisciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/clinical_data.txt
buisciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/comparatives.txt
buisciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/differential_expression.R
buisciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/lablog
buisciii/templates/rnaseq/ANALYSIS/DATE_ANALYSIS01_RNASEQ/02-differential_expression/time_series_differential_expression.R
buisciii/templates/rnaseq/DOC/candida_tropicalis_ncbi.yml
buisciii/templates/rnaseq/DOC/hg38_ensmbl_rnaseq.yml
buisciii/templates/rnaseq/DOC/hpc_slurm_rnaseq.config
buisciii/templates/rnaseq/RAW/README
buisciii/templates/rnaseq/REFERENCES/README
buisciii/templates/rnaseq/RESULTS/README
buisciii/templates/rnaseq/RESULTS/lablog_rnaseq_results
buisciii/templates/rnaseq/TMP/README
buisciii/templates/seek_and_destroy/ANALYSIS/lablog_seekndestroy
buisciii/templates/seek_and_destroy/ANALYSIS/ANALYSIS01_SEEK_DESTROY/lablog
buisciii/templates/seek_and_destroy/DOC/seek_destroy.config
buisciii/templates/seek_and_destroy/RAW/README
buisciii/templates/seek_and_destroy/REFERENCES/README
buisciii/templates/seek_and_destroy/RESULTS/lablog_seekndestroy_results
buisciii/templates/seek_and_destroy/TMP/README
buisciii/templates/snippy/ANALYSIS/lablog_snippy
buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/lablog
buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/01-fastqc/lablog
buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/02-preprocessing/lablog
buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/03-preprocQC/lablog
buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/04-snippy/lablog
buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/05-iqtree/lablog
buisciii/templates/snippy/ANALYSIS/ANALYSIS01_SNIPPY/99-stats/lablog
buisciii/templates/snippy/DOC/README
buisciii/templates/snippy/RAW/README
buisciii/templates/snippy/REFERENCES/README
buisciii/templates/snippy/RESULTS/README
buisciii/templates/snippy/RESULTS/lablog_snippy_results
buisciii/templates/snippy/TMP/README
buisciii/templates/taxprofiler/ANALYSIS/lablog_taxprofiler
buisciii/templates/taxprofiler/ANALYSIS/ANALYSIS01_TAXPROFILER/lablog
buisciii/templates/taxprofiler/DOC/databasesheet.csv
buisciii/templates/taxprofiler/DOC/taxprofiler.config
buisciii/templates/taxprofiler/RAW/README
buisciii/templates/taxprofiler/REFERENCES/README
buisciii/templates/taxprofiler/RESULTS/lablog_taxprofiler_results
buisciii/templates/taxprofiler/TMP/README
buisciii/templates/viralrecon/ANALYSIS/_02_create_run_percentage_Ns.sh
buisciii/templates/viralrecon/ANALYSIS/create_assembly_stats.R
buisciii/templates/viralrecon/ANALYSIS/create_summary_report.sh
buisciii/templates/viralrecon/ANALYSIS/deduplicate_long_table.sh
buisciii/templates/viralrecon/ANALYSIS/get_percentage_LDM.py
buisciii/templates/viralrecon/ANALYSIS/lablog_bam2fq
buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon
buisciii/templates/viralrecon/ANALYSIS/percentajeNs.py
buisciii/templates/viralrecon/ANALYSIS/remove_columns_mapping_table.sh
buisciii/templates/viralrecon/ANALYSIS/samples_ref.txt
buisciii/templates/viralrecon/ANALYSIS/sgene_metrics.sh
buisciii/templates/viralrecon/DOC/viralrecon.config
buisciii/templates/viralrecon/DOC/viralrecon_no_host_reads.config
buisciii/templates/viralrecon/DOC/viralrecon_params.yml
buisciii/templates/viralrecon/DOC/viralrecon_sars_nanopore.config
buisciii/templates/viralrecon/DOC/viralrecon_sars_nanopore_params.yml
buisciii/templates/viralrecon/RAW/README
buisciii/templates/viralrecon/REFERENCES/README
buisciii/templates/viralrecon/RESULTS/excel_generator.py
buisciii/templates/viralrecon/RESULTS/lablog_viralrecon_results
buisciii/templates/viralrecon/TMP/README
buisciii/templates/wgstrio/ANALYSIS/lablog_wgs
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/02-postprocessing/lablog
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/Merge_All.R
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/exomiser_configfile.yml
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/exomiser_configfile_exome.yml
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/exomiser_configfile_genes.yml
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/header_vep_final_annot.txt
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/inheritance_types.txt
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/lablog
buisciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/99-stats/lablog
buisciii/templates/wgstrio/DOC/hpc_slurm_sarek.config
buisciii/templates/wgstrio/REFERENCES/exomiser_exome.bed
buisciii/templates/wgstrio/REFERENCES/exomiser_exome_mod(no_probado).bed
buisciii/templates/wgstrio/REFERENCES/exomiser_exome_mod.interval_list
buisciii/templates/wgstrio/REFERENCES/exomiser_genes.bed
buisciii/templates/wgstrio/RESULTS/lablog_wgstrio_results
buisciii_tools.egg-info/PKG-INFO
buisciii_tools.egg-info/SOURCES.txt
buisciii_tools.egg-info/dependency_links.txt
buisciii_tools.egg-info/entry_points.txt
buisciii_tools.egg-info/not-zip-safe
buisciii_tools.egg-info/requires.txt
buisciii_tools.egg-info/top_level.txt
tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/percentajeNs.py
tests/archived/bi/services_and_colaborations/CNM/virology/SRVCNM786_20221205_GENOMEORTHORNAVIRAE02_mdfernandez_S/ANALYSIS/20221205_ANALYSIS02_METAGENOMIC_HUMAN/percentajeNs.py