| annotation/prokka.rules |
annotate_with_prokka |
| annotation/prokka.rules |
annotate_with_prokka_unfiltered_assembly |
| annotation/prokka.rules |
create_blast_database_from_protein_sequences |
| annotation/prokka.rules |
create_blast_database_from_contig_sequences |
| annotation/prokka.rules |
remove_fasta_part_from_gff |
| annotation/virulence.rules |
blast_virulence_protein_to_proteome_or_contigs |
| annotation/virulence.rules |
remove_redundancy_from_blast_results |
| annotation/virulence.rules |
extract_protein_sequences_from_blast_results |
| annotation/virulence.rules |
add_description_to_blast_results |
| annotation/virulence.rules |
merge_samples_summary |
| assembly/spades.rules |
correct_error_paired_reads_with_spades |
| assembly/spades.rules |
correct_error_single_reads_with_spades |
| assembly/spades.rules |
assemble_genome_paired_reads_with_spades |
| assembly/spades.rules |
assemble_genome_single_reads_with_spades |
| core_genome/bed_creation.rules |
extract_core_genome_parsnp_from_ref |
| downloading/fetch_references.rules |
get_refseq_urls_complete_genomes |
| downloading/fetch_references.rules |
download_all_complete_genomes_fasta |
| downloading/fetch_single_reference.rules |
download_reference_from_refseq |
| downloading/fetch_single_reference.rules |
download_reference_from_nucleotide |
| downloading/fetch_single_reference.rules |
get_strain_subvalue_identifier_reference |
| downloading/fetch_single_reference.rules |
download_gff_for_reference_from_refseq |
| downloading/fetch_virulence_factors.rules |
fetch_virulence_factors_from_uniprot_accessions |
| downloading/linking_references_for_core_genome_schemes.rules |
link_reference_genome_for_cgMLST |
| downloading/linking_references_for_core_genome_schemes.rules |
link_reference_genome_for_parsnp |
| downloading/linking_references_for_core_genome_schemes.rules |
link_full_genome |
| genotyping/freebayes_first_pass.rules |
genotype_with_freebayes_one_sample |
| genotyping/freebayes.rules |
genotype_with_freebayes_for_resistance |
| genotyping/freebayes.rules |
genotype_with_freebayes_on_all_samples |
| genotyping/freebayes.rules |
genotype_with_freebayes_one_sample_second_pass |
| genotyping/gatk.rules |
create_dictionary_for_reference |
| genotyping/gatk.rules |
genotype_with_HaplotypeCaller_GATK_BP_RESOLUTION |
| genotyping/gatk.rules |
merge_gvcf_files_with_GenomicsDBImport_GATK |
| genotyping/gatk.rules |
merge_gvcf_files_with_CombineGVCFs_GATK |
| genotyping/gatk.rules |
genotype_with_GenotypeGVCFs_GATK |
| mapping/bwa.rules |
map_paired_reads_with_bwa |
| mapping/bwa.rules |
map_single_reads_with_bwa |
| mapping/bwa.rules |
filter_reads_on_quality |
| mapping/bwa.rules |
remove_duplicates_from_mapping |
| mapping/find_closest_genomes.rules |
sketch_kmers_complete_genomes_with_mash |
| mapping/find_closest_genomes.rules |
calculate_distance_to_complete_genomes_with_mash |
| mapping/find_closest_genomes.rules |
extract_closest_genomes_to_all_samples |
| mapping/indexing_files.rules |
index_reference_fasta |
| mapping/indexing_files.rules |
index_bam_file |
| phylogeny/image_creation.rules |
convert_phylogeny_to_image_with_st |
| phylogeny/image_creation.rules |
convert_phylogeny_to_image_no_st |
| phylogeny/raxml.rules |
compute_phylogeny_with_raxml |
| phylogeny/raxml.rules |
compute_phylogeny_bootstraps_with_raxml |
| quality/assembly_filtering.rules |
copy_raw_assembly_to_reference_folder |
| quality/assembly_filtering.rules |
extract_contig_coverage |
| quality/assembly_filtering.rules |
filter_contigs_on_coverage |
| quality/assembly_filtering.rules |
extract_contigs_longer_than_500bp |
| quality/assembly_filtering.rules |
rename_contigs |
| quality/contamination.rules |
calculate_distance_paired_reads_from_refseq_genomes_with_mash |
| quality/contamination.rules |
calculate_distance_single_reads_from_refseq_genomes_with_mash |
| quality/contamination.rules |
get_taxonomy_from_mash_results |
| quality/contamination.rules |
format_distances_from_mash_results |
| quality/contamination.rules |
format_tsv_to_xlsx_mash_results |
| quality/contamination.rules |
merge_all_xlsx_mash_results |
| quality/trimmomatic.rules |
trim_paired_reads_with_trimmomatic |
| quality/trimmomatic.rules |
trim_single_reads_with_trimmomatic |
| read_manipulation/get_reads.rules |
copy_fastq_paired_from_link |
| read_manipulation/get_reads.rules |
copy_fastq_single_from_link |
| read_manipulation/get_sras.rules |
download_sra_single |
| read_manipulation/get_sras.rules |
download_sra_paired |
| report_generation/fastqc.rules |
assess_quality_single_reads_with_fastqc |
| report_generation/fastqc.rules |
assess_quality_paired_reads_with_fastqc |
| report_generation/fastqc.rules |
unzip_fastqc_single |
| report_generation/fastqc.rules |
unzip_fastqc_paired |
| report_generation/multiqc.rules |
create_multiqc_report_for_assembly |
| report_generation/multiqc.rules |
create_multiqc_report_for_mapping |
| report_generation/prepare_files_for_multiqc.rules |
copy_result_files_mapping_paired |
| report_generation/prepare_files_for_multiqc.rules |
copy_result_files_mapping_single |
| report_generation/prepare_files_for_multiqc.rules |
copy_result_files_assembly |
| report_generation/qualimap.rules |
assess_mapping_with_qualimap |
| report_generation/quast.rules |
calculate_assembly_statistics_with_quast |
| typing/mlst.rules |
determine_mlst |
| typing/mlst.rules |
merge_mlst_from_all_samples |
| typing/mlst.rules |
determine_mlst_reference_genome |
| typing/mlst.rules |
generate_xlsx_file_from_mlst_results |
| typing/snp_distance.rules |
distance_columns_to_matrix |
| typing/snp_distance.rules |
compute_minimum_spanning_tree_with_st |
| typing/snp_distance.rules |
compute_minimum_spanning_tree_no_st |
| vcf_manipulation/calculate_differences.rules |
calculate_pairwise_distances_by_type |
| vcf_manipulation/calculate_differences.rules |
get_pairwise_snps_positions_by_type |
| vcf_manipulation/calculate_differences.rules |
calculate_distance_with_ref_by_type |
| vcf_manipulation/calculate_differences.rules |
agregate_distances_from_joint_genotyping_by_type |
| vcf_manipulation/create_alignment_for_phylogeny.rules |
merge_multiallelic_by_sample |
| vcf_manipulation/create_alignment_for_phylogeny.rules |
extract_alternative_positions_and_unknown_positions |
| vcf_manipulation/create_alignment_for_phylogeny.rules |
create_consensus_sequence_by_sample |
| vcf_manipulation/create_alignment_for_phylogeny.rules |
concatenate_consensus_fasta_files_all_samples |
| vcf_manipulation/extract_cgMLST.rules |
extract_cgMLST_regions_from_vcf |
| vcf_manipulation/filtering.rules |
decompose_multiallelics_and_normalize |
| vcf_manipulation/filtering.rules |
filter_on_coverage |
| vcf_manipulation/filtering.rules |
filter_on_frequency_per_sample |
| vcf_manipulation/filtering.rules |
extract_allele_by_type_from_gatk_gvcfs |
| vcf_manipulation/filtering.rules |
extract_allele_by_type_from_freebayes_joint_genotyping |
| vcf_manipulation/filtering.rules |
extract_core_genome_parsnp |
| vcf_manipulation/indexing.rules |
compress_vcf |
| vcf_manipulation/indexing.rules |
index_vcf |
| vcf_manipulation/indexing.rules |
sort_vcf |
| vcf_manipulation/splitting_merging.rules |
extract_sample_entry_from_vcf |
| vcf_manipulation/splitting_merging.rules |
merge_all_samples_entries_into_vcf |
| vcf_manipulation/splitting_merging.rules |
merge_all_vcf_freebayes_first_pass |
| vcf_manipulation/splitting_merging.rules |
merge_freebayes_second_pass |
| annotation/resistance/format_xlsx.rules |
convert_tsv_to_xlsx |
| annotation/resistance/format_xlsx.rules |
merge_rgi_or_mykrobe_xlsx |
| annotation/resistance/m_tuberculosis.rules |
create_reference_lists_from_databases |
| annotation/resistance/m_tuberculosis.rules |
merge_nucleotides_and_codons_bed_files |
| annotation/resistance/m_tuberculosis.rules |
extract_all_locus_tags |
| annotation/resistance/m_tuberculosis.rules |
fetch_locus_tag_sequences_from_accession |
| annotation/resistance/m_tuberculosis.rules |
remove_shift_from_fasta_sequences |
| annotation/resistance/m_tuberculosis.rules |
shift_positions_from_genotype_vcf |
| annotation/resistance/m_tuberculosis.rules |
apply_genotype_to_fasta |
| annotation/resistance/m_tuberculosis.rules |
extract_mutated_positions |
| annotation/resistance/m_tuberculosis.rules |
extract_reference_positions |
| annotation/resistance/m_tuberculosis.rules |
format_resistance_results |
| annotation/resistance/m_tuberculosis.rules |
add_translation_to_mutated_codons |
| annotation/resistance/m_tuberculosis.rules |
format_mutated_nucleotides |
| annotation/resistance/m_tuberculosis.rules |
merge_mutated_nucleotides_and_codons |
| annotation/resistance/m_tuberculosis.rules |
merge_non_empty_results |
| annotation/resistance/mykrobe.rules |
search_resistance_paired_reads_with_mykrobe |
| annotation/resistance/mykrobe.rules |
search_resistance_single_reads_with_mykrobe |
| annotation/resistance/mykrobe.rules |
generate_mykrobe_tsv_file_from_json_file |
| annotation/resistance/rgi.rules |
search_resistance_with_rgi |
| annotation/resistance/rgi.rules |
extract_resistance_from_ontology |
| annotation/resistance/rgi.rules |
generate_rgi_tsv_file_from_json_file |
| annotation/resistance/summarize_results.rules |
summary_csv_excel_file |
| annotation/resistance/summarize_results.rules |
write_congruent_results_fasta |
| annotation/resistance/summarize_results.rules |
merge_summary_xlsx_files |