GEMSTONE_Plate_Swipes_Illumina_PE
v1.0.0
This workflow processes paired-end Illumina reads from plate swipes/plate bacterial metagenomes. It could also be used for broader bacterial metagenomic analysis. It removes human reads, performs QA and QC, and metagenomic assembly. Furthermore, it estimates taxa abundances with Kraken2 and Bracken, does strain-level identification with StrainGE, bins MAGs, performs AMR genotyping, and identifies plasmid contigs.
This workflow was based on the PHB v1.0.0 TheiaMeta workflow from Theiagen.
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Boolean Optional Default = false If true, aligns reads to the assembly, computes coverage, and retrieves aligned and unaligned reads.
File Optional Reference file for consensus calling, in FASTA format. If provided, performs consensus assembly and calling.
Boolean Optional Default = false If true, performs strain-level detection with StrainGE.
Boolean Optional Default = false If true, identifies taxa and estimates their abundance with Kraken2/Bracken.
Boolean Optional Default = false If true, performs genome binning and refinement of bins with metaWRAP.
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File Required FASTQ file with forward raw reads. Must be Illumina paired-end.
File Required FASTQ file with reverse raw reads. Must be Illumina paired-end.
String Required Name or ID of the sample.
String Required Genus or species name, as determined in the lab or by GAMBIT. Must be written in full, with whitespaces (e.g., Escherichia coli and not E. coli nor Escherichia_coli). Used to select a StrainGE reference database by matching the genus passed in this parameter with those in each database. Multiple genera are supported through a "/" separator, such as "Escherichia/Klebsiella" - this will call StrainGE twice, once using an Escherichia database, and once with a Klebsiella database.
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File Required TSV configuration file for StrainGE databases. It should be a table with two columns: one with the database genus name (e.g., Escherichia or Proteus), and another with the path to the tar archive with the StrainGE database for that genus. An example of this table is:
| Escherichia | gs://fc-secure-uuid/databases/strainge/escherichia_shigella.tar.gz |
|---|---|
| Shigella | gs://fc-secure-uuid/databases/strainge/escherichia_shigella.tar.gz |
| Pseudomonas | gs://fc-secure-uuid/databases/strainge/pseudomonas.tar.gz |
| Staphylococcus | gs://fc-secure-uuid/databases/strainge/staphylococcus.tar.gz |
| Proteus | gs://fc-secure-uuid/databases/strainge/proteus.tar.gz |
| Klebsiella | gs://fc-secure-uuid/databases/strainge/klebsiella.tar.gz |
| Acinetobacter | gs://fc-secure-uuid/databases/strainge/acinetobacter.tar.gz |
| Enterobacter | gs://fc-secure-uuid/databases/strainge/enterobacter.tar.gz |
| Enterococcus | gs://fc-secure-uuid/databases/strainge/enterococcus.tar.gz |
Int Optional Default = 5 Maximum number of strains searched by StrainGST.
Int Optional Default = 100 Disk size in Gb for the StrainGE task.
Int Optional Default = 4 Number of CPUs used in the StrainGE task.
Int Optional Default = 128 RAM in Gb for the StrainGE task.
Int Optional Default = 23 K-mer sized used when creating the StrainGST databases.
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File Optional Compressed Kraken2/Bracken database as a tar archive. Required if call_kraken is true. Please make sure that the archive contains all the files needed to run Bracken (refer to the Bracken docs).
Int Optional Default = 150 Input read length.
String Optional Default = "G" Taxonomic level for Bracken abundance estimation. Defaults to genus level (G). Other possible options are K (kingdom level), P (phylum), C (class), O (order), F (family), and S (species)
Int Optional Default = 256 Disk size in Gb for the Kraken2/Bracken task.
Int Optional Default = 4 Number of CPUs used in the Kraken2/Bracken task task.
Int Optional Default = 32 RAM in Gb for the Kraken2/Bracken task task.
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File Optional Compressed checkM database as a tar archive to be used in metaWRAP. Required if call_metawrap is true.
Int Optional Default = 80 Minimum completion of MAG bins, as determined by checkM, in percentage (i.e., a value of 80 means only bins with comlpetion greater or equal to 80% will be returned).
Int Optional Default = 10 Maximum contamination of MAG bins, as determined by checkM, in percentage (i.e., a value of 10 means only bins with contamination less than or equal to 10% will be returned).
Int Optional Default = 1000 Minimum length in bp of contigs included in the MAG bins returned by metaWRAP.
String Optional Default = "--metabat2 --maxbin2 --concoct" Contig binning tools used in metaWRAP, as flags. These flags are used in the metaWRAP binning command.
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String Version of the TheiaMeta workflow used.
String Analysis date.
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String Optional
Kraken2 version used.
String Optional Name of the Kraken2 and Bracken Docker image used.
File Optional Kraken2 report with taxa classifications.
File Optional Percentage of human-classified reads in the sample as determined by Kracken2.
File Optional Bracken report with estimated abundances per taxon.
String Optional Bracken version used.
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File Optional
FASTQ file of forward reads with human reads removed.
File Optional
FASTQ file of reverse reads with human reads removed.
String Optional Name of the NCBI Human Scrubber Docker image used.
Int Number of reads in read1.
Int Number of reads in read2.
Int Number of pairs of reads in read1 and read2 (raw reads).
String Version of fastq_scan used.
String Optional Name of the fastq_scan Docker image used.
Int Number of reads after QC in read1_clean.
Int Number of reads after QC in read2_clean.
Int Number of read pairs after QC in read1_clean and read2_clean (clean reads).
String Optional Version of trimmomatic used.
String Optional Name of the trimmomatic Docker image used.
File FASTQ file with forward cleaned reads, after QC and de-hosting.
File FASTQ file with reverse cleaned reads, after QC and de-hosting.
String Name of the BBDuk Docker image used.
Float Average length in bp of clean reads (read1_clean and read2_clean).
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File FASTA file of the final assembly (MAG). If no reference is used, it is the output from metaSPAdes + Pilon.
String Version of metaSPAdes used.
String Name of the metaSPAdes Docker image used.
String Version of minimap2 used.
String Name of the minimap2 Docker image used.
String Version of samtools used.
String Name of the samtools Docker image used.
String Version of Pilon used.
String Name of the Pilon Docker image used.
Int Assembly (MAG) length in bp.
Int Number of MAG contigs.
Int Length of the largest MAG contig in bp.
String Version of Quast used for assembly QC.
String Name of the Quast Docker image used for assembly QC.
Float Optional Percentage coverage of the reference genome (if provided).
Float Optional Mean depth of coverage of the final assembly. Returned only if output_additional_files is true.
String Optional Version of bedtools used for assembly QC. Returned only if output_additional_files is true.
String Optional Name of the bedtools Docker image used for assembly QC. Returned only if output_additional_files is true.
File Optional Unmapped forwards reads to the assembly. Returned only if output_additional_files is true.
File Optional Unmapped reverse reads to the assembly. Returned only if output_additional_files is true.
File Optional Mapped forwards reads to the assembly. Returned only if output_additional_files is true.
File Optional Mapped reverse reads to the assembly. Returned only if output_additional_files is true.
Float Optional Percentage of mapped reads to the assembly. Returned only if output_additional_files is true.
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Array[File] Optional Files with k-merized input reads. The size of the array depends on how many genera are assigned in lab_determined_genus, but the contents of each file should be the same. Returned only if call_strainge and straingst_found_db are true.
Array[File] Optional StrainGST databases used in each call to StrainGE. The size of the array depends on how many genera are assigned in lab_determined_genus. Returned only if call_strainge and straingst_found_db are true.
Boolean Optional Whether a StrainGST database matching the genera in lab_determined_genus was found. Returned only if call_strainge is true.
Array[File] Optional Text files of strains found by StrainGST when using each database. Returned only if call_strainge and straingst_found_db are true.
Array[File] Optional Reports with StrainGST statistics, including strain relative abundances, with each databased used. Returned only if call_strainge and straingst_found_db are true.
Array[File] Optional Concatenated references as FASTA files needed for downstream StrainGR analysis. The size of the array depends on how many genera are assigned in lab_determined_genus. Returned only if call_strainge and straingst_found_db are true.
Array[File] Optional Indexed BAM file of clean reads mapped to the concatenated references (in straingr_concat_fasta). The size of the array depends on how many genera are assigned in lab_determined_genus. Returned only if call_strainge and straingst_found_db are true.
Array[File] Optional HDF5 files with variant calling results from StrainGR. The size of the array depends on how many genera are assigned in lab_determined_genus. Returned only if call_strainge and straingst_found_db are true.
Array[File] Optional StrainGR reports with variant calling statistics. The size of the array depends on how many genera are assigned in lab_determined_genus. Returned only if call_strainge and straingst_found_db are true.
Array[String] Optional Name of the StrainGE Docker image used for strain-level detection. The size of the array depends on how many genera are assigned in lab_determined_genus. Returned only if call_strainge is true.
Array[String] Optional Version of StrainGE used for strain-level detection. The size of the array depends on how many genera are assigned in lab_determined_genus. Returned only if call_strainge is true.
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File MAG gene annotations from Bakta in GenBank format.
File MAG gene annotations from Bakta in GFF3 format.
File MAG gene annotations from Bakta in TSV format.
File Summary report of MAG gene annotation from Bakta.
String Version of Bakta used for MAG gene annotation.
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File TSV file with plasmid/chromosome classification of contigs from MOB-recon.
File TSV file with plasmid typing results from MOB-typer.
File FASTA file of chromosomal contigs in the MAG.
File FASTA file of plasmid contigs in the MAG.
String Name of the MOB-recon/MOB-suite Docker image used for plasmid identification.
String Version of MOB-recon/MOB-suite used for plasmid identification.
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File Report of all genes (virulence, stress, and AMR) found by AMRFinderPlus, as a TSV file.
File Report of AMR genes found by AMRFinderPlus, as a TSV file.
File Report of stress genes found by AMRFinderPlus, as a TSV file.
File Report of virulence genes found by AMRFinderPlus, as a TSV file.
String Comma separated list of core AMR genes found by AMRFinderPlus.
String Comma separated list of plus AMR genes found by AMRFinderPlus.
String Comma separated list of stress genes found by AMRFinderPlus.
String Comma separated list of virulence genes found by AMRFinderPlus.
String Comma separated list of classes of antimicrobial drugs for which AMR genes were found by AMRFinderPlus.
String Comma separated list of subclasses of antimicrobial drugs for which AMR genes were found by AMRFinderPlus.
String Version of AMRFinderPlus used for AMR genotyping.
String Version of AMRFinderPlus database used for AMR genotyping.
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String Optional Name of the metaWRAP Docker image used for MAG binning and bin refinement. Returned only if call_metawrap is true.
String Optional Version of metaWRAP used for MAG binning and bin refinement. Returned only if call_metawrap is true.
File Optional TSV with MAG bins statistics (including contamination and completeness). Returned only if call_metawrap is true.
Int Optional Number of MAG bins found by metaWRAP. Returned only if call_metawrap is true.
String Optional Contig binning tools used in metaWRAP, as flags. These flags were used in the metaWRAP binning command and provided as an input parameter. They are returned as outputs for record keeping. Returned only if call_metawrap is true.
Array[File] Optional MAG bins found by metaWRAP as FASTA files. Returned only if call_metawrap is true.
File Optional Bin assignments to each contig in the MAG, as a TSV file. Returned only if call_metawrap is true.
Marco Teixeira
Colin Worby
