ampliseq: add nanopore data

README.md

@@ -11,6 +11,49 @@ nf-core/test-datasets comes with documentation in the `docs/` directory:
 01. [Add a new  test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
 02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
 
+## Contents
+
+### `expected/`
+
+Expected sequences and abundances to compare the observed to the expected (pipeline) outcome.
+
+- `expected_abundances.tsv` & `expected_sequences.fasta`: made-up expected data for Illumina MiSeq v2 data
+- `*ZymoBIOMICS*`: ZymoBIOMICS mock communities, unique 16S sequences, abundances summed up for multiple 16S copies
+
+ZymoBIOMICS mock communities, theoretical Composition Based on Genomic DNA: 
+
+- `D6305`: Listeria monocytogenes - 12%, Pseudomonas aeruginosa - 12%, Bacillus subtilis - 12%, Escherichia coli - 12%, Salmonella enterica - 12%, Lactobacillus fermentum - 12%, Enterococcus faecalis - 12%, Staphylococcus aureus - 12%, Saccharomyces cerevisiae - 2%, and Cryptococcus neoformans - 2%. 
+- `D6311`: Listeria monocytogenes - 89.1%, Pseudomonas aeruginosa - 8.9%, Bacillus subtilis - 0.89%, Saccharomyces cerevisiae - 0.89%, Escherichia coli - 0.089%, Salmonella enterica - 0.089%, Lactobacillus fermentum - 0.0089%, Enterococcus faecalis - 0.00089%, Cryptococcus neoformans - 0.00089%, and Staphylococcus aureus - 0.000089%.
+
+### `samplesheets/`
+
+Sample sheets pointing to raw data files in `testdata/`. Additionally metadata sheets corresponding to the sample sheets.
+
+### `testdata/`
+
+Raw sequencing data of various sequencing technologies.
+Additionally tiny reference datasets are deposited here.
+Some legacy metdata and sample sheets ("Manifest*") are still in that folder, that shall be (re)moved eventually.
+
+#### Illumina
+
+- `*_L001_R1_001.fastq.gz`: MiSeq v2 data
+- `novaseq*.fq.gz`: binned quality
+- `multiregion*.fq.gz`: 5R data amplified with several primers
+- `testdoubleprimers*.fastq.gz`: contains multiple primer copies
+
+#### ionTorrent
+
+- `*_elembio_R[1/2].fastq.gz`: single-end ionTorrent reads
+
+#### PacBio
+
+- `pb*-its-reads_of_insert.fastq.gz`: PacBio reads of the ITS region
+
+#### Nanopore
+
+- `<sample>_<mock-dataset>_16SBarcodingKit24V14_SQK-16S114.24_r10.4.1_sup.chopper.<number-of-reads>.fastq.gz`: Zymo Standard Communities D6305 or D6311, Rapid sequencing DNA - 16S Barcoding Kit 24 V14 (SQK-16S114.24), Flongle, Basecalling using SUP v4.3.0 model. Filtered with Chopper (-q 16) and either the first 1000 (number-of-reads:1000), or first 1000 and last 2000 reads (number-of-reads:3000). _This dataset was generated by the Core Facility Genomics Tübingen and the Institute for Medical Microbiology and Hygiene, University Hospital Tübingen._
+
 ## Support
 
 For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging).

expected/D6305-D6311_ZymoBIOMICS.STD.refseq.v2.ssrRNAs.unique.abundance.tsv

@@ -0,0 +1,27 @@
+ID	Log1	Log2	Log3	Std1	Std2	Std3	copies	log_expected_percentage_per-taxon	std_expected_percentage_per-taxon
+Bacillus_subtilis_16S_4x_1-8-9-10	3.56	3.56	3.56	0.48	0.48	0.48	4	0.89	0.12
+Bacillus_subtilis_16S_2x_2-3	1.78	1.78	1.78	0.24	0.24	0.24	2	0.89	0.12
+Bacillus_subtilis_16S_4	0.89	0.89	0.89	0.12	0.12	0.12	1	0.89	0.12
+Bacillus_subtilis_16S_5	0.89	0.89	0.89	0.12	0.12	0.12	1	0.89	0.12
+Bacillus_subtilis_16S_6	0.89	0.89	0.89	0.12	0.12	0.12	1	0.89	0.12
+Bacillus_subtilis_16S_7	0.89	0.89	0.89	0.12	0.12	0.12	1	0.89	0.12
+Cryptococcus_neoformans_18S_170924	0	0	0	0	0	0	1	0.00089	0.02
+Cryptococcus_neoformans_Mitochondria_ssrRNA	0	0	0	0	0	0	1		0.02
+Enterococcus_faecalis_16S_4x_1-2-3-4	0.00356	0.00356	0.00356	0.48	0.48	0.48	4	0.00089	0.12
+Escherichia_coli_16S_4x_1-3-5-8	0.356	0.356	0.356	0.48	0.48	0.48	4	0.089	0.12
+Escherichia_coli_16S_2x_2-7	0.178	0.178	0.178	0.24	0.24	0.24	2	0.089	0.12
+Escherichia_coli_16S_4	0.089	0.089	0.089	0.12	0.12	0.12	1	0.089	0.12
+Lactobacillus_fermentum_16S_3x_1-2-4	0.0267	0.0267	0.0267	0.36	0.36	0.36	3	0.0089	0.12
+Lactobacillus_fermentum_16S_3	0.0089	0.0089	0.0089	0.12	0.12	0.12	1	0.0089	0.12
+Lactobacillus_fermentum_16S_5	0.0089	0.0089	0.0089	0.12	0.12	0.12	1	0.0089	0.12
+Listeria_monocytogenes_16S_4x_1-4-5-6	356.4	356.4	356.4	0.48	0.48	0.48	4	89.1	0.12
+Listeria_monocytogenes_16S_2	89.1	89.1	89.1	0.12	0.12	0.12	1	89.1	0.12
+Listeria_monocytogenes_16S_3	89.1	89.1	89.1	0.12	0.12	0.12	1	89.1	0.12
+Pseudomonas_aeruginosa_16S_4x_1-2-3-4	35.6	35.6	35.6	0.48	0.48	0.48	4	8.9	0.12
+Saccharomyces_cerevisiae_18S_170924	0	0	0	0	0	0	1	0.89	0.02
+Saccharomyces_cerevisiae_mitochondria_ssrRNA	0	0	0	0	0	0	1	0.89	0.02
+Salmonella_enterica_16S_1	0.089	0.089	0.089	0.12	0.12	0.12	1	0.089	0.12
+Salmonella_enterica_16S_6x_2-3-4-5-6	0.534	0.534	0.534	0.72	0.72	0.72	6	0.089	0.12
+Staphylococcus_aureus_16S_1	0.000089	0.000089	0.000089	0.12	0.12	0.12	1	0.000089	0.12
+Staphylococcus_aureus_16S_2	0.000089	0.000089	0.000089	0.12	0.12	0.12	1	0.000089	0.12
+Staphylococcus_aureus_16S_4x_3-4-5-6	0.000356	0.000356	0.000356	0.48	0.48	0.48	4	0.000089	0.12