Add abromics bacterial hybrid assembly and annotation workflow

workflows/genome-assembly/bacterial-genomic-hybrid-long-reads-assembly/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /abromics_genomic_hybrid_long_reads.ga
+  authors:
+  - name: Pierre
+    alternateName: pimarin
+    email: mailto:[email protected]
+    familyName: MARIN
+    orcid: 0000-0002-8304-138X
+  - name: abromics-consortium
+    email: mailto:[email protected]
+    url: https://www.abromics.fr/

workflows/genome-assembly/bacterial-genomic-hybrid-long-reads-assembly/CHANGELOG.md

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+# Changelog
+
+## [0.1] 2024-01-24
+
+### Automatic update
+- First release of bacterial genomic workflow from the ABRomics French project (www.abromics.fr)[https://www.abromics.fr/]

workflows/genome-assembly/bacterial-genomic-hybrid-long-reads-assembly/README.md

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+# Bacterial genome assembly and annotation to hybrid long reads assembly
+
+This workflow use paired-end illumina fastq(.gz) files and long-read (tested on nanopore) input (fastq.gz) and make some analysis to assembly bacterial genomes and annotate genomes to extract antimicrobial informations.
+
+The main steps are:
+1. Quality control and trimming
+2. Taxonomic assignation on trimmed data
+3. Assembly and polishing raw reads to a final contig fasta file
+4. Quality control of the assembly
+5. Genomic annotation:
+    - Genomic annotation
+    - Integron identification
+    - Plasmid gene identification
+    - Inserted Element (IS) detection
+    - Antimicrobial resistance gene identification
+    - Virulence gene identification
+
+## Tools used
+1. Quality control and trimming
+    - fastp QC control and trimming for short reads
+    - FastQC and filtlong for QC and trimming of long reads
+2. Taxonomic assignation on long read data
+    - kraken2 assignation
+    - bracken to restimate abundance to the species level
+    - recentrifuge to make a krona chart    
+3. Assembly raw reads to a final contig fasta file
+    - flye and polipolish to use the illumina reads
+4. Quality control of the assembly
+    - Quast
+    - Bandage to plot assembly graph
+    - Refseqmasher to identify the closed reference genome
+5. Genomic annotation:
+    - Genomic annotation: Bakta
+    - Integron identification: IntegronFinder2
+    - Plasmid gene identification: Plasmidfinder
+    - Inserted Element (IS) detection: ISEScan
+    - Antimicrobial resistance gene identification: staramr to blast against resfinder and plasmidfinder database
+    - Virulence gene identification: abricate with VFDB_A database
+
+The multiQC tool is used to aggregate all QC result into only 1 report.
+
+
+
+## inputs
+
+1. Paired-end illumina rax reads in fastq(.gz) format.
+2. Single long read in fastq(.gz) format.
+
+## Outputs
+1. Quality control:
+    - quality report
+    - trimmed raw reads
+2. Taxonomic assignation:
+    - Tabular report of identified species
+    - Tabular file with assigned read to a taxonomic level
+    - Krona chart to illustrate species diversity of the sample
+3. Assembly:
+    - polished assembly with contigs in fasta
+    - Mapped read on assembly in bam format
+    - Graph assembly in gfa format
+4. Quality of Assembly:
+    - Assembly report
+    - Assembly Graph
+    - Tabular result of closed reference genomes
+5. Genomic annotation:
+    - Genomic annotation:
+        - genome annotation in tabular, gff and several other formats
+        - annotation plot
+        - nucleotide and protein sequences identified
+        - summary of genomic identified elements
+    - Integron identification:
+        - integron identification in tabular format and a summary
+    - Plasmid gene identification :
+        - plasmid gene identified and associated blast hits
+    - Inserted Element (IS) detection :
+        - IS element list in tabular format
+        - is hits in fasta format
+        - ORF hits in protein and nucleotide fasta format
+        - IS annotation gff format
+    - Antimicrobial resistance gene identification
+        - AMR gene list
+        - MLST typing
+        - Plasmid gene identification
+        - Blast hits
+    - Virulence gene identification
+        - Gene identification in tabular format

workflows/genome-assembly/bacterial-genomic-hybrid-long-reads-assembly/abromics_genomic_hybrid_long_reads_tests.yml

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+- doc: Test outline for abromics_genomic_hybrid_long_reads
+  job:
+    paired_r2:
+      class: File
+      path: test-data/paired_r2.fastqsanger.gz
+      filetype: fastqsanger.gz
+    paired_r1:
+      class: File
+      path: test-data/paired_r1.fastqsanger.gz
+      filetype: fastqsanger.gz
+    long_reads_input:
+      class: File
+      path: test-data/long_reads_input.fastqsanger.gz
+      filetype: fastqsanger.gz
+    select_plasmidfinder_database: plasmidfinder_314d85f_2023_03_17
+    select_amrfinderplus_to_bakta_database: amrfinderplus_V3.11_2023-04-17.1
+    select_bakta_database: V5.0light_2023-02-20
+    select_ncbi_taxonomy_database: ncbi-2015-10-05
+    select_kraken2_database: 2022-02-02T162959Z_silva_kmer-len_35_minimizer-len_31_minimizer-spaces_6_load-factor_0.7
+    select_bracken_database: 2022-02-02T162959Z_silva_kmer-len_35_minimizer-len_31_minimizer-spaces_6_load-factor_0.7
+  outputs:
+    bandage_contig_graph_plot:
+      path: test-data/bandage_contig_graph_plot.svg
+      compare: sim_size
+      delta: 30000
+    bakta_aminoacid_sequence_faa:
+      path: test-data/bakta_aminoacid_sequence_faa.fasta
+      compare: sim_size
+      delta: 30000
+    bakta_annotation_log:
+      path: test-data/bakta_annotation_log.txt
+      compare: sim_size
+      delta: 1000
+    bakta_annotation_plot:
+      path: test-data/bakta_annotation_plot.svg
+      compare: sim_size
+      delta: 30000
+    bakta_annotation_json:
+      path: test-data/bakta_annotation_json.json
+      compare: sim_size
+      delta: 30000
+    bakta_summary_text:
+      path: test-data/bakta_summary_text.txt
+      compare: sim_size
+      delta: 1000
+    bakta_hypothetical_faa:
+      path: test-data/bakta_hypothetical_faa.fasta
+      compare: sim_size
+      delta: 30000
+    bakta_hypothetical_tabular:
+      path: test-data/bakta_hypothetical_tabular.tabular
+      compare: sim_size
+      delta: 30000
+    bakta_nucleotide_sequence_fasta:
+      path: test-data/bakta_nucleotide_sequence_fasta.fasta
+      compare: sim_size
+      delta: 30000
+    bakta_assembly_fasta:
+      path: test-data/bakta_assembly_fasta.fasta
+      compare: sim_size
+      delta: 30000
+    bakta_annotation_embl:
+      path: test-data/bakta_annotation_embl.tabular
+      compare: sim_size
+      delta: 30000
+    bakta_annotation_gbff:
+      path: test-data/bakta_annotation_gbff.tabular
+      compare: sim_size
+      delta: 30000
+    bakta_annotation_gff3:
+      path: test-data/bakta_annotation_gff3.gff3
+      compare: sim_size
+      delta: 30000
+    bakta_annotation_tabular:
+      path: test-data/bakta_annotation_tabular.tabular
+      compare: sim_size
+      delta: 30000
+    quast_report_tabular:
+      path: test-data/quast_report_tabular.tabular
+      compare: sim_size
+      delta: 10000
+    popypolish_fasta:
+      path: test-data/popypolish_fasta.fasta
+      compare: sim_size
+      delta: 60000
+    aligned_R2_bam:
+      path: test-data/aligned_R2_bam.qname_input_sorted.bam
+      compare: sim_size
+      delta: 60000
+    aligned_R1_bam:
+      path: test-data/aligned_R1_bam.qname_input_sorted.bam
+      compare: sim_size
+      delta: 60000
+    recentrifuge_report_html:
+      path: test-data/recentrifuge_report_html.html
+      compare: sim_size
+      delta: 30000
+    bracken_report_tsv:
+      path: test-data/bracken_report_tsv.tabular
+    flye_assembly_graph:
+      path: test-data/flye_assembly_graph.graph_dot
+      compare: sim_size
+      delta: 30000
+    flye_assembly_fasta:
+      path: test-data/flye_assembly_fasta.fasta
+      compare: sim_size
+      delta: 30000
+    kraken_report_reads:
+      path: test-data/kraken_report_reads.tabular
+    kraken_report_tabular:
+      path: test-data/kraken_report_tabular.tabular
+    quality_check_after_text:
+      path: test-data/quality_check_after_text.txt
+    fastp_report_json:
+      path: test-data/fastp_report_json.json
+      compare: sim_size
+      delta: 30000
+    fastp_trimmed_R2:
+      path: test-data/fastp_trimmed_R2.fastqsanger.gz
+    fastp_trimmed_R1:
+      path: test-data/fastp_trimmed_R1.fastqsanger.gz
+    quality_report_before_text:
+      path: test-data/quality_report_before_text.txt
+      compare: diff
+      lines_diff: 7