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Co-authored-by: Matthias Hörtenhuber <[email protected]>

main.nf

@@ -17,7 +17,7 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { AMPLISEQ  } from './workflows/ampliseq'
+include { AMPLISEQ                } from './workflows/ampliseq'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_ampliseq_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_ampliseq_pipeline'
 

nextflow_schema.json

@@ -31,7 +31,6 @@
                 "input_folder": {
                     "type": "string",
                     "format": "directory-path",
-                    "mimetype": "text/tsv",
                     "fa_icon": "fas fa-dna",
                     "description": "Path to folder containing zipped FastQ files",
                     "help_text": "Path to folder containing compressed fastq files.\n\nExample for input data organization from one sequencing run with two samples, paired-end data:\n\n```bash\ndata\n  \u251c\u2500sample1_1_L001_R1_001.fastq.gz\n  \u251c\u2500sample1_1_L001_R2_001.fastq.gz\n  \u251c\u2500sample2_1_L001_R1_001.fastq.gz\n  \u2514\u2500sample2_1_L001_R2_001.fastq.gz\n```\n\nPlease note the following requirements:\n\n1. The path must be enclosed in quotes\n2. The folder must contain gzip compressed demultiplexed fastq files. If the file names do not follow the default (`\"/*_R{1,2}_001.fastq.gz\"`), please check `--extension`.\n3. Sample identifiers are extracted from file names, i.e. the string before the first underscore `_`, these must be unique\n4. If your data is scattered, produce a sample sheet\n5. All sequencing data should originate from one sequencing run, because processing relies on run-specific error models that are unreliable when data from several sequencing runs are mixed. Sequencing data originating from multiple sequencing runs requires additionally the parameter `--multiple_sequencing_runs` and a specific folder structure.\n\nRelated parameters are:\n- `--pacbio` and `--iontorrent` if the sequencing data is PacBio data or IonTorrent data (default expected: paired-end Illumina data)\n- `--single_end` if the sequencing data is single-ended Illumina data (default expected: paired-end Illumina data)\n- `--multiple_sequencing_runs` if the sequencing data originates from multiple sequencing runs\n- `--extension` if the sequencing file names do not follow the default (`\"/*_R{1,2}_001.fastq.gz\"`)\n- Choose an appropriate reference taxonomy for the type of amplicon (16S/18S/ITS/CO1) (default: DADA2 assignTaxonomy and 16S rRNA sequence database)"