├── .github └── workflows │ └── build.yaml ├── Dockerfile ├── LICENSE ├── README.md ├── Singularity.def ├── db_schema_patches ├── 1_to_2.sql └── 2_to_3.sql ├── multipass ├── README.md ├── bashrc ├── install_mysql.sh ├── install_singularity.sh └── launch_vm.sh ├── nextflow ├── fake_remove_contam.nf ├── generic_pipeline.nf ├── import.nf ├── mykrobe_predict.nf ├── qc.nf ├── remove_contam.nf └── variant_call.nf ├── python ├── .gitignore ├── README.md ├── clockwork │ ├── __init__.py │ ├── common_data.py │ ├── contam_remover.py │ ├── cortex.py │ ├── data_finder.py │ ├── db.py │ ├── db_connection.py │ ├── db_maker.py │ ├── db_schema.py │ ├── ena │ │ ├── __init__.py │ │ ├── dataset_submitter.py │ │ ├── object_creator.py │ │ ├── submission_receipt.py │ │ ├── submit_files.py │ │ └── xml_create.py │ ├── ena_downloader.py │ ├── fake_contam_remover.py │ ├── fastqc.py │ ├── fqtools.py │ ├── gvcf.py │ ├── het_snp_caller.py │ ├── isolate_dir.py │ ├── lock_file.py │ ├── mykrobe.py │ ├── picard.py │ ├── read_map.py │ ├── read_pair_importer.py │ ├── read_trim.py │ ├── reference_dir.py │ ├── samtools_qc.py │ ├── simple_vcf_merger.py │ ├── spreadsheet_helper.py │ ├── spreadsheet_importer.py │ ├── spreadsheet_validator.py │ ├── tasks │ │ ├── __init__.py │ │ ├── cortex.py │ │ ├── db_add_mykrobe_panel.py │ │ ├── db_finished_pipeline_update.py │ │ ├── db_finished_pipeline_update_failed_jobs.py │ │ ├── ena_download.py │ │ ├── ena_submit_reads.py │ │ ├── fake_remove_contam.py │ │ ├── fake_remove_contam_make_jobs_tsv.py │ │ ├── fastqc.py │ │ ├── find_data.py │ │ ├── generic_pipeline_make_jobs_tsv.py │ │ ├── gvcf_from_minos_and_samtools.py │ │ ├── gvcf_to_fasta.py │ │ ├── import_read_pair.py │ │ ├── import_spreadsheet.py │ │ ├── make_empty_db.py │ │ ├── make_import_spreadsheet.py │ │ ├── map_reads.py │ │ ├── minos_make_multi_sample_input.py │ │ ├── mykrobe_predict.py │ │ ├── mykrobe_predict_make_jobs_tsv.py │ │ ├── qc_make_jobs_tsv.py │ │ ├── reference_prepare.py │ │ ├── remove_contam.py │ │ ├── remove_contam_make_jobs_tsv.py │ │ ├── samtools_cortex_vcf_merge.py │ │ ├── samtools_qc.py │ │ ├── trim_reads.py │ │ ├── validate_spreadsheet.py │ │ ├── variant_call_make_jobs_tsv.py │ │ ├── variant_call_one_sample.py │ │ └── version.py │ ├── tests │ │ ├── contam_remover_test.py │ │ ├── cortex_test.py │ │ ├── data │ │ │ ├── contam_remover │ │ │ │ ├── load_metadata_file.tsv │ │ │ │ ├── read_mapped_and_wanted.reads.fq │ │ │ │ ├── read_mapped_and_wanted.ref.fa │ │ │ │ ├── read_mapped_and_wanted.sam │ │ │ │ ├── run.expected_counts.tsv │ │ │ │ ├── run.metadata.tsv │ │ │ │ ├── run.no_match_are_wanted.contam_1.fq │ │ │ │ ├── run.no_match_are_wanted.contam_2.fq │ │ │ │ ├── run.no_match_are_wanted.counts.tsv │ │ │ │ ├── run.no_match_are_wanted.wanted_1.fq │ │ │ │ ├── run.no_match_are_wanted.wanted_2.fq │ │ │ │ ├── run.no_match_not_wanted.contam_1.fq │ │ │ │ ├── run.no_match_not_wanted.contam_2.fq │ │ │ │ ├── run.no_match_not_wanted.no_match_1.fq │ │ │ │ ├── run.no_match_not_wanted.no_match_2.fq │ │ │ │ ├── run.no_match_not_wanted.wanted_1.fq │ │ │ │ ├── run.no_match_not_wanted.wanted_2.fq │ │ │ │ ├── run.reads_1.fq │ │ │ │ ├── run.reads_2.fq │ │ │ │ ├── run.ref.fa │ │ │ │ ├── run.sam │ │ │ │ ├── sam_to_fastq.reads_1.fq │ │ │ │ ├── sam_to_fastq.reads_2.fq │ │ │ │ ├── sam_to_fastq.ref.fa │ │ │ │ ├── sam_to_fastq.sam │ │ │ │ └── write_read_counts_by_group_file.expected.tsv │ │ │ ├── cortex │ │ │ │ ├── Reference │ │ │ │ │ ├── ref.fa │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ ├── make_files.sh │ │ │ │ ├── make_ref_fastas.py │ │ │ │ ├── mutated.fa │ │ │ │ ├── reads.fq │ │ │ │ ├── replace_sample_name_in_vcf.expect.vcf │ │ │ │ ├── replace_sample_name_in_vcf.in.bad1.vcf │ │ │ │ ├── replace_sample_name_in_vcf.in.bad2.vcf │ │ │ │ ├── replace_sample_name_in_vcf.in.bad3.vcf │ │ │ │ └── replace_sample_name_in_vcf.in.vcf │ │ │ ├── data_finder │ │ │ │ ├── write_pipeline_data_to_file.mykrobe_predict.tsv │ │ │ │ ├── write_pipeline_data_to_file.qc.tsv │ │ │ │ ├── write_pipeline_data_to_file.remove_contam.ref.1.tsv │ │ │ │ ├── write_pipeline_data_to_file.remove_contam.set2.tsv │ │ │ │ ├── write_pipeline_data_to_file.remove_contam.tsv │ │ │ │ ├── write_pipeline_data_to_file.remove_contam.v0.1.1.tsv │ │ │ │ ├── write_pipeline_data_to_file.remove_contam.with_internal_ids.tsv │ │ │ │ ├── write_pipeline_data_to_file.variant_call.tsv │ │ │ │ ├── write_seqrep_data_to_file.set2.tsv │ │ │ │ └── write_seqrep_data_to_file.tsv │ │ │ ├── db.ini │ │ │ ├── db │ │ │ │ ├── load_success_jobs_file.no_pool_column.tsv │ │ │ │ ├── load_success_jobs_file.with_pool_column.tsv │ │ │ │ ├── update_finished_pipeline_run_failed_jobs.jobs.tsv │ │ │ │ ├── update_finished_pipeline_run_failed_jobs.success.tsv │ │ │ │ ├── update_finished_pipeline_run_failed_jobs_pooled.jobs.tsv │ │ │ │ ├── update_finished_pipeline_run_failed_jobs_pooled.success.tsv │ │ │ │ ├── update_finished_pipeline_run_remove_contam │ │ │ │ │ └── counts.tsv │ │ │ │ ├── update_qc_stats_pipeline_root │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 01 │ │ │ │ │ │ └── 2 │ │ │ │ │ │ └── Pipelines │ │ │ │ │ │ └── 3 │ │ │ │ │ │ └── qc │ │ │ │ │ │ └── 1.0.0 │ │ │ │ │ │ ├── fastqc │ │ │ │ │ │ ├── fastqc_reads_1_fastqc │ │ │ │ │ │ │ ├── fastqc_data.txt │ │ │ │ │ │ │ ├── fastqc_report.html │ │ │ │ │ │ │ └── summary.txt │ │ │ │ │ │ └── fastqc_reads_2_fastqc │ │ │ │ │ │ │ ├── fastqc_data.txt │ │ │ │ │ │ │ ├── fastqc_report.html │ │ │ │ │ │ │ └── summary.txt │ │ │ │ │ │ └── samtools_qc │ │ │ │ │ │ ├── het_snps.summary.tsv │ │ │ │ │ │ └── samtools_qc.stats │ │ │ │ └── update_remove_contam_stats.counts.tsv │ │ │ ├── db_connection │ │ │ │ ├── config.good.ini │ │ │ │ ├── config.good_with_port.ini │ │ │ │ ├── config.missing_user.ini │ │ │ │ └── config.no_db_login_header.ini │ │ │ ├── ena │ │ │ │ ├── dataset_submitter │ │ │ │ │ ├── config.ini │ │ │ │ │ ├── db.cnf │ │ │ │ │ ├── get_data_from_db │ │ │ │ │ │ ├── Pipeline_refs │ │ │ │ │ │ │ ├── 1 │ │ │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ │ │ ├── Pipeline_root │ │ │ │ │ │ │ └── 00 │ │ │ │ │ │ │ │ └── 00 │ │ │ │ │ │ │ │ └── 00 │ │ │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ │ ├── reads.contam.43.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.contam.43.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.43.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.43.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.43.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.43.2.fq.gz │ │ │ │ │ │ │ │ │ └── reads.remove_contam.43.counts.tsv │ │ │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ │ │ └── 03 │ │ │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ ├── reads.contam.49.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.contam.49.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.49.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.49.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.49.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.49.2.fq.gz │ │ │ │ │ │ │ │ └── reads.remove_contam.49.counts.tsv │ │ │ │ │ │ ├── Reads │ │ │ │ │ │ │ ├── reads.1.1.fq.gz │ │ │ │ │ │ │ └── reads.1.2.fq.gz │ │ │ │ │ │ ├── Reference │ │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ │ │ ├── db.cnf │ │ │ │ │ │ ├── make_files.sh │ │ │ │ │ │ └── mysql.dump │ │ │ │ │ └── run │ │ │ │ │ │ ├── Pipeline_refs │ │ │ │ │ │ ├── 1 │ │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ │ │ ├── Pipeline_root │ │ │ │ │ │ └── 00 │ │ │ │ │ │ │ └── 00 │ │ │ │ │ │ │ └── 00 │ │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ ├── reads.contam.43.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.contam.43.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.43.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.43.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.43.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.43.2.fq.gz │ │ │ │ │ │ │ │ └── reads.remove_contam.43.counts.tsv │ │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ │ ├── 2 │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── 03 │ │ │ │ │ │ │ └── 4 │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── 04 │ │ │ │ │ │ │ └── 5 │ │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ └── 05 │ │ │ │ │ │ │ └── 6 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.49.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.49.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.49.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.49.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.49.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.49.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.49.counts.tsv │ │ │ │ │ │ ├── Reads │ │ │ │ │ │ ├── reads.1.1.fq.gz │ │ │ │ │ │ └── reads.1.2.fq.gz │ │ │ │ │ │ ├── Reference │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ │ │ ├── cryptic_data_template.xlsx │ │ │ │ │ │ ├── db.cnf │ │ │ │ │ │ ├── make_files.sh │ │ │ │ │ │ └── mysql.dump │ │ │ │ ├── object_creator │ │ │ │ │ └── conf.ini │ │ │ │ ├── submission_receipt │ │ │ │ │ ├── init.bad_receipt.xml │ │ │ │ │ └── init.good_receipt.xml │ │ │ │ ├── submit_files │ │ │ │ │ ├── conf.bad.no_ena_login.ini │ │ │ │ │ ├── conf.bad.no_password.ini │ │ │ │ │ ├── conf.bad.no_user.ini │ │ │ │ │ └── conf.good.ini │ │ │ │ └── xml_create │ │ │ │ │ ├── element_tree_to_file.xml │ │ │ │ │ ├── make_add_submission_xml.with_broker.xml │ │ │ │ │ ├── make_add_submission_xml.xml │ │ │ │ │ ├── make_experiment_xml.xml │ │ │ │ │ ├── make_paired_fastq_run_xml.xml │ │ │ │ │ ├── make_project_xml.xml │ │ │ │ │ └── make_sample_xml.xml │ │ │ ├── ena_downloader │ │ │ │ ├── load_data_infile.bad_columns.tsv │ │ │ │ ├── load_data_infile.good.tsv │ │ │ │ ├── load_data_infile.repeat_accesion.tsv │ │ │ │ ├── load_data_infile.repeat_sample_name.tsv │ │ │ │ ├── rename_files.data.tsv │ │ │ │ ├── rename_files │ │ │ │ │ ├── ERR0000012 │ │ │ │ │ │ ├── ERR0000012_1.fastq.gz │ │ │ │ │ │ └── ERR0000012_2.fastq.gz │ │ │ │ │ ├── ERR0000013 │ │ │ │ │ │ ├── ERR0000013_1.fastq.gz │ │ │ │ │ │ └── ERR0000013_2.fastq.gz │ │ │ │ │ ├── ERR0000050 │ │ │ │ │ │ ├── ERR0000050_1.fastq.gz │ │ │ │ │ │ └── ERR0000050_2.fastq.gz │ │ │ │ │ ├── ERS0000020 │ │ │ │ │ │ └── ERR0000014 │ │ │ │ │ │ │ ├── ERR0000014_1.fastq.gz │ │ │ │ │ │ │ └── ERR0000014_2.fastq.gz │ │ │ │ │ └── ERS0000042 │ │ │ │ │ │ ├── ERR0001000 │ │ │ │ │ │ ├── ERR0001000_1.fastq.gz │ │ │ │ │ │ └── ERR0001000_2.fastq.gz │ │ │ │ │ │ └── ERR0001001 │ │ │ │ │ │ ├── ERR0001001_1.fastq.gz │ │ │ │ │ │ └── ERR0001001_2.fastq.gz │ │ │ │ └── write_import_tsv.expected.tsv │ │ │ ├── fake_contam_remover │ │ │ │ ├── reads_1.fq.gz │ │ │ │ ├── reads_2.fq.gz │ │ │ │ └── write_counts_tsv.expect.tsv │ │ │ ├── fastqc │ │ │ │ ├── clean_outdir │ │ │ │ │ ├── fastqc_reads_1_fastqc.html │ │ │ │ │ ├── fastqc_reads_1_fastqc.zip │ │ │ │ │ ├── fastqc_reads_1_fastqc │ │ │ │ │ │ ├── Icons │ │ │ │ │ │ │ ├── error.png │ │ │ │ │ │ │ ├── fastqc_icon.png │ │ │ │ │ │ │ ├── tick.png │ │ │ │ │ │ │ └── warning.png │ │ │ │ │ │ ├── Images │ │ │ │ │ │ │ ├── adapter_content.png │ │ │ │ │ │ │ ├── duplication_levels.png │ │ │ │ │ │ │ ├── per_base_n_content.png │ │ │ │ │ │ │ ├── per_base_quality.png │ │ │ │ │ │ │ ├── per_base_sequence_content.png │ │ │ │ │ │ │ ├── per_sequence_gc_content.png │ │ │ │ │ │ │ ├── per_sequence_quality.png │ │ │ │ │ │ │ └── sequence_length_distribution.png │ │ │ │ │ │ ├── fastqc.fo │ │ │ │ │ │ ├── fastqc_data.txt │ │ │ │ │ │ ├── fastqc_report.html │ │ │ │ │ │ └── summary.txt │ │ │ │ │ ├── fastqc_reads_2_fastqc.html │ │ │ │ │ ├── fastqc_reads_2_fastqc.zip │ │ │ │ │ └── fastqc_reads_2_fastqc │ │ │ │ │ │ ├── Icons │ │ │ │ │ │ ├── error.png │ │ │ │ │ │ ├── fastqc_icon.png │ │ │ │ │ │ ├── tick.png │ │ │ │ │ │ └── warning.png │ │ │ │ │ │ ├── Images │ │ │ │ │ │ ├── adapter_content.png │ │ │ │ │ │ ├── duplication_levels.png │ │ │ │ │ │ ├── per_base_n_content.png │ │ │ │ │ │ ├── per_base_quality.png │ │ │ │ │ │ ├── per_base_sequence_content.png │ │ │ │ │ │ ├── per_sequence_gc_content.png │ │ │ │ │ │ ├── per_sequence_quality.png │ │ │ │ │ │ └── sequence_length_distribution.png │ │ │ │ │ │ ├── fastqc.fo │ │ │ │ │ │ ├── fastqc_data.txt │ │ │ │ │ │ ├── fastqc_report.html │ │ │ │ │ │ └── summary.txt │ │ │ │ ├── gather_all_stats │ │ │ │ │ ├── fastqc_reads_1_fastqc │ │ │ │ │ │ ├── fastqc_data.txt │ │ │ │ │ │ ├── fastqc_report.html │ │ │ │ │ │ └── summary.txt │ │ │ │ │ └── fastqc_reads_2_fastqc │ │ │ │ │ │ ├── fastqc_data.txt │ │ │ │ │ │ ├── fastqc_report.html │ │ │ │ │ │ └── summary.txt │ │ │ │ ├── reads_1.fq │ │ │ │ ├── reads_2.fq │ │ │ │ └── stats_from_report.txt │ │ │ ├── fqtools │ │ │ │ ├── count.1.fq │ │ │ │ ├── count.2.fq │ │ │ │ ├── validate.bad.fq │ │ │ │ ├── validate.bad.pair.1.fq │ │ │ │ ├── validate.bad.pair.2.fq │ │ │ │ ├── validate.ok.pair.1.fq │ │ │ │ └── validate.ok.pair.2.fq │ │ │ ├── gvcf │ │ │ │ ├── gvcf_from_minos_vcf_and_samtools_gvcf.minos.vcf │ │ │ │ ├── gvcf_from_minos_vcf_and_samtools_gvcf.out.vcf │ │ │ │ ├── gvcf_from_minos_vcf_and_samtools_gvcf.ref.fa │ │ │ │ ├── gvcf_from_minos_vcf_and_samtools_gvcf.ref.fa.fai │ │ │ │ ├── gvcf_from_minos_vcf_and_samtools_gvcf.samtools.vcf │ │ │ │ ├── gvcf_to_fasta.fa │ │ │ │ └── gvcf_to_fasta.vcf │ │ │ ├── het_snp_caller │ │ │ │ ├── filter_vcf_and_count_snps.expect.vcf │ │ │ │ ├── filter_vcf_and_count_snps.in.vcf │ │ │ │ ├── run.bam │ │ │ │ ├── run.expect.per_contig.tsv │ │ │ │ ├── run.expect.summary.tsv │ │ │ │ ├── run.make_files.sh │ │ │ │ ├── run.make_ref_fastas.py │ │ │ │ ├── run.reads_1.fq.gz │ │ │ │ ├── run.reads_2.fq.gz │ │ │ │ ├── run.ref.fa │ │ │ │ ├── run.ref.fa.amb │ │ │ │ ├── run.ref.fa.ann │ │ │ │ ├── run.ref.fa.bwt │ │ │ │ ├── run.ref.fa.fai │ │ │ │ ├── run.ref.fa.pac │ │ │ │ ├── run.ref.fa.sa │ │ │ │ ├── run.ref_to_make_reads.fa │ │ │ │ ├── write_reports.per_contig │ │ │ │ └── write_reports.summary │ │ │ ├── mykrobe │ │ │ │ ├── run_predict.json │ │ │ │ ├── run_predict.probes.fa │ │ │ │ └── run_predict.reads.fq.gz │ │ │ ├── nextflow_fake_remove_contam │ │ │ │ ├── Pipeline_root │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ └── reads.original.1.2.fq.gz │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ └── reads.original.1.2.fq.gz │ │ │ │ │ │ ├── 03 │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ └── reads.original.1.2.fq.gz │ │ │ │ │ │ └── 04 │ │ │ │ │ │ └── 4 │ │ │ │ │ │ └── Reads │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ └── reads.original.1.2.fq.gz │ │ │ │ ├── db.cnf │ │ │ │ ├── make_files.sh │ │ │ │ └── mysql.dump │ │ │ ├── nextflow_generic_pipeline │ │ │ │ ├── Pipeline_refs │ │ │ │ │ ├── 1 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ │ └── 2 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ ├── Pipeline_root │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ ├── 03 │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ └── 04 │ │ │ │ │ │ └── 4 │ │ │ │ │ │ └── Reads │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ ├── Reads │ │ │ │ │ ├── reads.1.1.fq.gz │ │ │ │ │ └── reads.1.2.fq.gz │ │ │ │ ├── Reference │ │ │ │ │ ├── ref.fa │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ ├── db.cnf │ │ │ │ ├── make_files.sh │ │ │ │ ├── make_ref_fastas.py │ │ │ │ ├── mysql.dump │ │ │ │ └── script.pl │ │ │ ├── nextflow_import │ │ │ │ └── dropbox │ │ │ │ │ ├── site_A.import.xlsx │ │ │ │ │ ├── site_A.reads.1_1.fq.gz │ │ │ │ │ ├── site_A.reads.1_1.fq.gz.md5 │ │ │ │ │ ├── site_A.reads.1_2.fq.gz │ │ │ │ │ ├── site_A.reads.2_1.fq.gz │ │ │ │ │ ├── site_A.reads.2_1.fq.gz.md5 │ │ │ │ │ ├── site_A.reads.2_2.fq.gz │ │ │ │ │ ├── site_A.reads.2_2.fq.gz.md5 │ │ │ │ │ ├── site_A.reads.3_1.fq.gz │ │ │ │ │ ├── site_A.reads.3_1.fq.gz.md5 │ │ │ │ │ ├── site_A.reads.3_2.fq.gz │ │ │ │ │ ├── site_A.reads.3_2.fq.gz.md5 │ │ │ │ │ ├── site_B.import.xlsx │ │ │ │ │ ├── site_B.reads.1_1.fq.gz │ │ │ │ │ ├── site_B.reads.1_1.fq.gz.md5 │ │ │ │ │ ├── site_B.reads.1_2.fq.gz │ │ │ │ │ ├── site_B.reads.1_2.fq.gz.md5 │ │ │ │ │ ├── site_B.reads.2_1.fq.gz │ │ │ │ │ ├── site_B.reads.2_1.fq.gz.md5 │ │ │ │ │ ├── site_B.reads.2_2.fq.gz │ │ │ │ │ └── site_B.reads.2_2.fq.gz.md5 │ │ │ ├── nextflow_mykrobe_predict │ │ │ │ ├── Pipeline_refs │ │ │ │ │ ├── 1 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ │ └── 2 │ │ │ │ │ │ └── data.json │ │ │ │ ├── Pipeline_root │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ ├── 03 │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ └── 04 │ │ │ │ │ │ └── 4 │ │ │ │ │ │ └── Reads │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ ├── Reads │ │ │ │ │ ├── reads.1.1.fq.gz │ │ │ │ │ └── reads.1.2.fq.gz │ │ │ │ ├── db.cnf │ │ │ │ ├── make_files.sh │ │ │ │ └── mysql.dump │ │ │ ├── nextflow_qc │ │ │ │ ├── Pipeline_refs │ │ │ │ │ ├── 1 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ │ └── 2 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ ├── Pipeline_root │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.43.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.43.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.43.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.43.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.43.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.43.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.43.counts.tsv │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.45.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.45.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.45.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.45.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.45.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.45.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.45.counts.tsv │ │ │ │ │ │ ├── 03 │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.47.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.47.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.47.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.47.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.47.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.47.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.47.counts.tsv │ │ │ │ │ │ └── 04 │ │ │ │ │ │ └── 4 │ │ │ │ │ │ └── Reads │ │ │ │ │ │ ├── reads.contam.49.1.fq.gz │ │ │ │ │ │ ├── reads.contam.49.2.fq.gz │ │ │ │ │ │ ├── reads.original.49.1.fq.gz │ │ │ │ │ │ ├── reads.original.49.2.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.49.1.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.49.2.fq.gz │ │ │ │ │ │ └── reads.remove_contam.49.counts.tsv │ │ │ │ ├── Reads │ │ │ │ │ ├── reads.1.1.fq.gz │ │ │ │ │ └── reads.1.2.fq.gz │ │ │ │ ├── Reference │ │ │ │ │ ├── ref.fa │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ ├── db.cnf │ │ │ │ ├── make_files.sh │ │ │ │ └── mysql.dump │ │ │ ├── nextflow_remove_contam │ │ │ │ ├── Pipeline_refs │ │ │ │ │ └── 1 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ ├── Pipeline_root │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.original.43.1.fq.gz │ │ │ │ │ │ │ └── reads.original.43.2.fq.gz │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.original.45.1.fq.gz │ │ │ │ │ │ │ └── reads.original.45.2.fq.gz │ │ │ │ │ │ ├── 03 │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.original.47.1.fq.gz │ │ │ │ │ │ │ └── reads.original.47.2.fq.gz │ │ │ │ │ │ └── 04 │ │ │ │ │ │ └── 4 │ │ │ │ │ │ └── Reads │ │ │ │ │ │ ├── reads.original.49.1.fq.gz │ │ │ │ │ │ └── reads.original.49.2.fq.gz │ │ │ │ ├── Reads │ │ │ │ │ ├── reads.1.1.fq.gz │ │ │ │ │ └── reads.1.2.fq.gz │ │ │ │ ├── Reference │ │ │ │ │ ├── ref.fa │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ ├── db.cnf │ │ │ │ ├── make_files.sh │ │ │ │ └── mysql.dump │ │ │ ├── nextflow_variant_call │ │ │ │ ├── Pipeline_refs │ │ │ │ │ ├── 1 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ └── remove_contam_metadata.tsv │ │ │ │ │ └── 2 │ │ │ │ │ │ ├── ref.fa │ │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ ├── Pipeline_root │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ └── 00 │ │ │ │ │ │ ├── 01 │ │ │ │ │ │ └── 1 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ ├── 02 │ │ │ │ │ │ └── 2 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.2.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ │ ├── reads.remove_contam.2.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.2.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.2.counts.tsv │ │ │ │ │ │ ├── 03 │ │ │ │ │ │ └── 3 │ │ │ │ │ │ │ └── Reads │ │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ │ │ └── 04 │ │ │ │ │ │ └── 4 │ │ │ │ │ │ └── Reads │ │ │ │ │ │ ├── reads.contam.1.1.fq.gz │ │ │ │ │ │ ├── reads.contam.1.2.fq.gz │ │ │ │ │ │ ├── reads.original.1.1.fq.gz │ │ │ │ │ │ ├── reads.original.1.2.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.1.1.fq.gz │ │ │ │ │ │ ├── reads.remove_contam.1.2.fq.gz │ │ │ │ │ │ └── reads.remove_contam.1.counts.tsv │ │ │ │ ├── Reads │ │ │ │ │ ├── reads.1.1.fq.gz │ │ │ │ │ └── reads.1.2.fq.gz │ │ │ │ ├── Reference │ │ │ │ │ ├── ref.fa │ │ │ │ │ ├── ref.fa.amb │ │ │ │ │ ├── ref.fa.ann │ │ │ │ │ ├── ref.fa.bwt │ │ │ │ │ ├── ref.fa.fai │ │ │ │ │ ├── ref.fa.pac │ │ │ │ │ ├── ref.fa.sa │ │ │ │ │ ├── ref.k31.ctx │ │ │ │ │ ├── ref.stampy.sthash │ │ │ │ │ └── ref.stampy.stidx │ │ │ │ ├── db.cnf │ │ │ │ ├── make_files.sh │ │ │ │ ├── make_ref_fastas.py │ │ │ │ ├── mysql.dump │ │ │ │ ├── truth_ref.fa │ │ │ │ ├── truth_ref.fa.amb │ │ │ │ ├── truth_ref.fa.ann │ │ │ │ ├── truth_ref.fa.bwt │ │ │ │ ├── truth_ref.fa.pac │ │ │ │ └── truth_ref.fa.sa │ │ │ ├── picard │ │ │ │ └── mark_duplicates.in.bam │ │ │ ├── read_map │ │ │ │ ├── flagstat │ │ │ │ ├── markdup.flagstat │ │ │ │ ├── reads.1.fq │ │ │ │ ├── reads.2.fq │ │ │ │ ├── reads_set_1.1.fq │ │ │ │ ├── reads_set_1.2.fq │ │ │ │ ├── reads_set_2.1.fq │ │ │ │ ├── reads_set_2.2.fq │ │ │ │ ├── reads_set_3.1.fq │ │ │ │ ├── reads_set_3.2.fq │ │ │ │ ├── ref.fa │ │ │ │ ├── ref.fa.amb │ │ │ │ ├── ref.fa.ann │ │ │ │ ├── ref.fa.bwt │ │ │ │ ├── ref.fa.pac │ │ │ │ ├── ref.fa.sa │ │ │ │ ├── rmdup.flagstat │ │ │ │ ├── secondary_hits_removed.reads_1.fq │ │ │ │ ├── secondary_hits_removed.reads_2.fq │ │ │ │ ├── secondary_hits_removed.ref.fa │ │ │ │ ├── secondary_hits_removed.ref.fa.amb │ │ │ │ ├── secondary_hits_removed.ref.fa.ann │ │ │ │ ├── secondary_hits_removed.ref.fa.bwt │ │ │ │ ├── secondary_hits_removed.ref.fa.pac │ │ │ │ └── secondary_hits_removed.ref.fa.sa │ │ │ ├── read_pair_importer │ │ │ │ ├── copy_reads_file.fq │ │ │ │ ├── run.bad_reads.1.fq │ │ │ │ ├── run.bad_reads.2.fq │ │ │ │ ├── run.reads.1.fq │ │ │ │ └── run.reads.2.fq │ │ │ ├── read_trim │ │ │ │ ├── trimmomatic_reads_1.fq │ │ │ │ ├── trimmomatic_reads_2.fq.gz │ │ │ │ ├── trimmomatic_reads_expect_1.fq │ │ │ │ └── trimmomatic_reads_expect_2.fq │ │ │ ├── ref_Mtb │ │ │ │ ├── NC_000962.3.fa │ │ │ │ └── NC_000962.3.gb │ │ │ ├── reference_dir │ │ │ │ ├── add_remove_contam_metadata_tsv.ref.extra_in_tsv.tsv │ │ │ │ ├── add_remove_contam_metadata_tsv.ref.fa │ │ │ │ ├── add_remove_contam_metadata_tsv.ref.good.tsv │ │ │ │ ├── add_remove_contam_metadata_tsv.ref.missing_from_tsv.tsv │ │ │ │ ├── make_index_files.ref.expected.fa │ │ │ │ └── make_index_files.ref.in.fa.gz │ │ │ ├── samtools_qc │ │ │ │ ├── het_snps_report.tsv │ │ │ │ ├── reads.1.fq │ │ │ │ ├── reads.2.fq │ │ │ │ ├── ref.fa │ │ │ │ ├── ref.fa.amb │ │ │ │ ├── ref.fa.ann │ │ │ │ ├── ref.fa.bwt │ │ │ │ ├── ref.fa.fai │ │ │ │ ├── ref.fa.pac │ │ │ │ ├── ref.fa.sa │ │ │ │ ├── sam │ │ │ │ └── stats_from_report.txt │ │ │ ├── simple_vcf_merger │ │ │ │ ├── NC_000962.3.fa │ │ │ │ ├── cortex.vcf │ │ │ │ ├── expect.vcf │ │ │ │ └── samtools.vcf │ │ │ ├── spreadsheet_helper │ │ │ │ ├── load_data_from_spreadsheet.tsv │ │ │ │ ├── load_data_from_spreadsheet.xlsx │ │ │ │ ├── load_data_from_spreadsheet_bad_column_names.xlsx │ │ │ │ └── load_data_from_spreadsheet_wrong_field_number.xlsx │ │ │ ├── spreadsheet_importer │ │ │ │ └── run.dropbox │ │ │ │ │ ├── import.xlsx │ │ │ │ │ ├── reads.1_1.fq │ │ │ │ │ ├── reads.1_2.fq │ │ │ │ │ ├── reads.2_1.fq │ │ │ │ │ ├── reads.2_1.fq.md5 │ │ │ │ │ ├── reads.2_2.fq │ │ │ │ │ └── reads.2_2.fq.md5 │ │ │ ├── spreadsheet_validator │ │ │ │ ├── reads_1_1.fq │ │ │ │ ├── reads_1_2.fq │ │ │ │ ├── reads_2_1.fq │ │ │ │ ├── reads_2_2.fq │ │ │ │ ├── run.in.bad.xlsx │ │ │ │ └── run.in.good.xlsx │ │ │ └── utils │ │ │ │ ├── load_md5_from_file.bad_linux │ │ │ │ ├── load_md5_from_file.bad_mac │ │ │ │ ├── load_md5_from_file.good_linux │ │ │ │ ├── load_md5_from_file.good_mac │ │ │ │ ├── md5.txt │ │ │ │ └── rsync_and_md5.txt │ │ ├── data_finder_test.py │ │ ├── db_connection_test.py │ │ ├── db_maker_test.py │ │ ├── db_test.py │ │ ├── ena │ │ │ ├── __init__.py │ │ │ ├── dataset_submitter_test.py │ │ │ ├── object_creator_test.py │ │ │ ├── submission_receipt_test.py │ │ │ ├── submit_files_test.py │ │ │ └── xml_create_test.py │ │ ├── ena_downloader_test.py │ │ ├── fake_contam_remover_test.py │ │ ├── fastqc_test.py │ │ ├── fqtools_test.py │ │ ├── gvcf_test.py │ │ ├── het_snp_caller_test.py │ │ ├── isolate_dir_test.py │ │ ├── lock_file_test.py │ │ ├── mykrobe_test.py │ │ ├── nextflow_fake_remove_contam_test.py │ │ ├── nextflow_generic_pipeline_test.py │ │ ├── nextflow_helper.py │ │ ├── nextflow_import_test.py │ │ ├── nextflow_mykrobe_predict_test.py │ │ ├── nextflow_qc_test.py │ │ ├── nextflow_remove_contam_test.py │ │ ├── nextflow_variant_call_test.py │ │ ├── picard_test.py │ │ ├── read_map_test.py │ │ ├── read_pair_importer_test.py │ │ ├── read_trim_test.py │ │ ├── reference_dir_test.py │ │ ├── samtools_qc_test.py │ │ ├── simple_vcf_merger_test.py │ │ ├── spreadsheet_helper_test.py │ │ ├── spreadsheet_importer_test.py │ │ ├── spreadsheet_validator_test.py │ │ ├── utils_test.py │ │ └── var_call_one_sample_pipeline_test.py │ ├── utils.py │ └── var_call_one_sample_pipeline.py ├── scripts │ └── clockwork └── setup.py ├── scripts ├── download_tb_reference_files.pl ├── get_genome_from_ncbi.pl └── install_dependencies.sh └── vagrant ├── README.md └── Vagrantfile /.github/workflows/build.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/clockwork/HEAD/.github/workflows/build.yaml -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/iqbal-lab-org/clockwork/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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