MAD4HatTeR Pipeline Parameters This workflow runs the entire MAD4HatTeR pipeline, processing amplicon sequencing FASTQ data to produce allele tables, resistance markers, and other outputs. Input Parameters | Input Name | Description | Type | Required | Default | |--------------------------|----------------------------------------------------------------------------------------------------------------------------------|---------------|----------|-------------------------------| | pools | List of pool or panel names. Options: MAD4HatTeR ["D1.1","R1.1","R2.1","R1.2","v1","v2"], PfPHAST ["M1.1","M2.1","M1.addon"], Other ["4cast","ama1"] | Array[String] | Yes | - | | forward_fastqs | List of forward FASTQ files. Order must match reverse_fastqs | Array[File] | Yes | - | | reverse_fastqs | List of reverse FASTQ files. Order must match forward_fastqs | Array[File] | Yes | - | | output_directory | Folder name for outputs | String | Yes | - | | amplicon_info_files | Amplicon info file(s) to define the panel information. If not provided then the pre-defined panel info for the pools will be used. | Array[File] | No | - | | targeted_reference_files | Targeted reference file(s). If not provided then the pre-defined reference sequences for the pools will be used. | Array[File] | No | - | | refseq_fasta | Path to targeted reference sequences. If not provided then the pre-defined reference sequences for the pools will be used. | File | No | - | | genome | Path to genome file. If not provided then the pre-defined reference sequences for the pools will be used. | File | No | - | | omega_a | Level of statistical evidence required for DADA2 to infer a new ASV | Float | No | 0.000... 001 | | dada2_pool | Pooling method for DADA2 to process ASVs | String | No | pseudo | | band_size | Limit on net cumulative number of insertions in DADA2 | Int | No | 16 | | max_ee | Limit on number of expected errors within a read in DADA2 | Int | No | 3 | | cutadapt_minlen | Minimum length for cutadapt | Int | No | 100 | | gtrim | If true, --nextseq-trim will be used to trim trailing G in cutadapt. | Bool | No | false | | quality_score | The quality score threshold to apply in cutadapt. | Int | No | 20 | | allowed_errors | Allowed errors for cutadapt | Int | No | 0 | | just_concatenate | If true, just concatenate reads | Boolean | No | false | | mask_tandem_repeats | Mask tandem repeats | Boolean | No | true | | mask_homopolymers | Mask homopolymers | Boolean | No | true | | masked_fasta | Masked FASTA file | File | No | - | | principal_resmarkers | Principal resistance markers file | File | No | - | | resmarkers_info_tsv | Resistance markers info TSV file | File | No | - | | dada2_additional_memory | Additional memory (in GB) to be added to the provided memory used in the DADA2 runtime configuration | Int | No | 0 | | dada2_runtime_size | DADA2 runtime size [small, medium, large]. Should be based on the size of the input dataset. Will be calculated if not provided | String | No | - | | docker_image | The Docker image to use | String | No | eppicenter/mad4hatter:develop | Pipeline Outputs For more information about the pipeline outputs see here. | Output Name | Description | Type | |----------------------------------|----------------------------------------------------------------------------------------------|--------| | final_allele_table_cloud_path | Path to the final allele table in the cloud output directory | String | | sample_coverage_cloud_path | Path to the sample coverage file in the cloud output directory | String | | amplicon_coverage_cloud_path | Path to the amplicon coverage file in the cloud output directory | String | | dada2_clusters_cloud_path | Path to the DADA2 clusters file in the cloud output directory | String | | resmarkers_output_cloud_path | Path to the resistance markers output file in the cloud output directory | String | | resmarkers_by_locus_cloud_path | Path to the resistance markers by locus file in the cloud output directory | String | | microhaps_cloud_path | Path to the microhaplotypes file in the cloud output directory | String | | new_mutations_cloud_path | Path to the new mutations file in the cloud output directory | String | | amplicon_info_cloud_path | Path to the amplicon info file in the cloud output directory | String | | reference_fasta_cloud_path | Path to the reference FASTA file in the cloud output directory | String | | resmarkers_file_cloud_path | Path to the resistance markers file in the cloud output directory | String |