Merge pull request #1990 from Vicbeg/rnastructurome

Add 3 test data and description of data for nf-core/rnastructurome

Author: Vicbeg

.gitignore

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+.DS_Store

README.md

@@ -32,6 +32,44 @@ git remote set-branches --add origin [remote-branch]
 git fetch
 ```
 
+## rnastructurome pipeline test data
+
+Test data for the [nf-core/rnastructurome](https://github.com/nf-core/rnastructurome) pipeline lives on the `rnastructurome` branch under `testdata/`.
+
+There are three independent test datasets, each exercising a different route through the pipeline:
+
+- **`test_genome`**: tests the genome-alignment route. Run with `-profile test,docker`.
+- **`test_transcriptome`**: tests the transcriptome-alignment route, including the `structextract` module. Run with `-profile test_transcriptome,docker`.
+- **`test_prokaryote`**: tests the `jackknife` and `eval` modules using prokaryote 16S rRNA data and a known reference structure for that rRNA. Run with `-profile test_prokaryote,conda`.
+
+**Human (HEK293) data** — the `test_genome` and `test_transcriptome` datasets are both derived from a real HEK293 dataset (accessions listed below). Reads aligning to the mitochondrial gene RNR1 (`ENST00000389680.2`) were extracted from the full dataset to create this small test data.
+- For the genome route, the full GRCh38 FASTA and GTF were each subsetted to just the MT chromosome.
+- For the transcriptome route, the RNR1 transcript was extracted from the full GRCh38 transcriptome FASTA, and the same MT GTF was reused.
+
+**Prokaryote (E. coli) data** — reads aligning to 16S rRNA were extracted from a real *E. coli* dataset (accession listed below) to create the tiny prokaryote dataset. The reference structure for 16S rRNA was supplied by Danny Incarnato and is used by both the `jackknife` and `eval` modules. The FASTA and GTF files were created from the 16S rRNA reference structure.
+
+### Directory structure
+
+```
+testdata/
+├── HEK293T_untreated_r1.fastq.gz       # shared SHAPE-seq reads (untreated, GSM4333255)
+├── HEK293T_treated_r1.fastq.gz         # shared SHAPE-seq reads (treated, GSM4333256)
+├── test_genome/                         
+│   ├── Homo_sapiens.GRCh38.MT.fa       # human mitochondrial chromosome 
+│   ├── Homo_sapiens.GRCh38.MT.gtf      # MT genome annotation
+│   └── samplesheet.genome_test.csv
+├── test_transcriptome/                  
+│   ├── Homo_sapiens.GRCh38.ENST00000389680.fa  # single-transcript FASTA (MT-RNR1)
+│   ├── Homo_sapiens.GRCh38.MT.gtf              # MT genome annotation 
+│   └── samplesheet.transcriptome_test.csv
+└── test_prokaryote/                     
+    ├── 16S_rRNA.fa                      # E. coli 16S rRNA FASTA
+    ├── 16S_rRNA.gtf                     # matching single-transcript GTF
+    ├── 16S_rRNA.reference.db            # dot-bracket reference structure for rf-eval/rf-jackknife
+    ├── E_coli_DH5a_treated.16S_rRNA.fastq.gz  # treated, GSM7885842
+    └── samplesheet.prokaryote_test.csv
+```
+
 ## 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).

testdata/HEK293T_treated_r1.fastq.gz

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+sample,sample_id,fastq_1,fastq_2,method,principle,sample_group,condition,replicate,organism,pH,adapter_3p,adapter_5p,umi_pattern
+HEK293T_untreated_r1,GSM4333255,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnastructurome/testdata/HEK293T_untreated_r1.fastq.gz,,SHAPE,RT-stop,HEK293T,untreated,1,Homo sapiens,7.5,,,
+HEK293T_treated_r1,GSM4333256,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/rnastructurome/testdata/HEK293T_treated_r1.fastq.gz,,SHAPE,RT-stop,HEK293T,treated,1,Homo sapiens,7.5,,,

testdata/HEK293T_untreated_r1.fastq.gz

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+>16S_rRNA Escherichia coli 16S ribosomal RNA
+AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA

testdata/test_genome/Homo_sapiens.GRCh38.MT.fa

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+16S_rRNA	testdata	gene	1	1542	.	+	.	gene_id "16S_rRNA"; gene_name "16S_rRNA"; gene_biotype "rRNA";
+16S_rRNA	testdata	transcript	1	1542	.	+	.	gene_id "16S_rRNA"; transcript_id "16S_rRNA"; gene_name "16S_rRNA"; transcript_biotype "rRNA";
+16S_rRNA	testdata	exon	1	1542	.	+	.	gene_id "16S_rRNA"; transcript_id "16S_rRNA"; exon_id "16S_rRNA.exon1"; exon_number "1";

testdata/test_genome/Homo_sapiens.GRCh38.MT.gtf

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+>16S_rRNA
+AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA
+........(((((...[[[.))))).((((.((((((.(((((((((....(((.(((..(((..((.((..((((((((((....))))))).)))))..)))))......(((......(((((((..((...(((((((.(.((.....((((((....))))))......)).).....(((....)))....((((((..((....)))))))).)))))))..)).)))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...(((((....))))).)))).)).))))))..((((......((((....)))).....)))).[.(.(((((...(....((((((((.......)))))))).....)....)))))...])..((((([[[...(((((.....((.]]])).......)))))))))).))))))))))..........((([[...(.((((...(((.(((((((.(((((((((((.....((((((.....))))))...)))))))))..)))))))))...((((((((...((((((((...((((((((...(((......)))......))))))))...).......((....)).)))))))..)))).))))...)))...))))....((((((...((...((((.........))))...))))))))..........((((((..((((((((((((.....))))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]]..(((((.(((((((.((..((((((.((((((((((....((((........))))........(((((((......(((((((..(((((((....))))))).(.((....)).)))))).))..((.((((..((((((.((...(((((((((....)))..((((......))))..)))))).....((((.(((((((...((..(((.....)))))....)))))))..((.(((((.....))))).)).....))))....)).).)))...))))))))....)))))))...)).)))))))).)...(((((((.....(((..((...(((....)))...))....))).....)))))))......(....(((((((........)))))))....).....))))).....(((((((.........)))))))......))...)))))))))).))..(.(..((.(.((((.(((..((((((((((((....((((((.((((..((....)).))))))))))...))))))))))))..))).))))..).))...)..).((((((((((....)))))))))).............