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Merged
mashehu merged 6 commits into from
Oct 7, 2026
Merged

Add a full test samplesheet #1972

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de3d207
Create full test samplesheet
BenjaminWehnert1008 Apr 7, 2026
ff2b9b5
Delete samplesheet/GID1A_full_test
BenjaminWehnert1008 Apr 7, 2026
40e72ca
Create full test samplesheet
BenjaminWehnert1008 Apr 7, 2026
75127b9
Add deepmutscan full-size samplesheet
BenjaminWehnert1008 Oct 6, 2026
f1a29a4
[automated] Fix code linting
nf-core-bot Oct 6, 2026
9218d6c
Add GID1A AlphaFold structure for deepmutscan
BenjaminWehnert1008 Oct 7, 2026
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12 changes: 12 additions & 0 deletions README.md
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Expand Up @@ -10,6 +10,18 @@ nf-core is a collection of high quality Nextflow pipelines. This repository cont

The principle for nf-core test data is as small as possible, as large as necessary. Please see the [guidelines](https://nf-co.re/docs/contributing/test_data_guidelines) for more detailed information. Always ask for guidance on the [nf-core slack](https://nf-co.re/join) before adding new test data.

## nf-core/deepmutscan test data

| File | Description |
| --- | --- |
| `testdata/GID1A.fasta` | Reference amplicon containing the GID1A ORF (UniProt Q9MAA7); the mutagenised reading frame is `352-1383`. |
| `testdata/reads/GID1A_{input,output}{1,2}_50k_{1,2}.fastq.gz` | 50,000 read-pair subsamples of the GluePCA GID1A-GAI shotgun DMS libraries below, used by `-profile test`. |
| `testdata/GID1A_AFDB.pdb` | AlphaFold DB model of GID1A (UniProt Q9MAA7, https://alphafold.ebi.ac.uk/entry/Q9MAA7), used by both profiles for the variant effect inspection tool. CC-BY-4.0, © EMBL-EBI & Google DeepMind. |
| `samplesheet/GID1A_test.csv` | Samplesheet for `-profile test` (2 input + 2 output replicates, the subsampled reads). |
| `samplesheet/GID1A_full.csv` | Samplesheet for `-profile test_full`: all 6 libraries (3 input, 3 output at 2500 uM GA3), ~480M read pairs, linked directly from ENA. |

Source: ENA project [PRJEB110196](https://www.ebi.ac.uk/ena/browser/view/PRJEB110196) (runs ERR16945046-ERR16945051), publicly available under the INSDC data policy. The full samplesheet points at the submitted FASTQ files, which ENA archives for all six runs.

## Documentation

nf-core/test-datasets comes with documentation in the `docs/` directory:
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7 changes: 7 additions & 0 deletions samplesheet/GID1A_full.csv
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sample,type,replicate,file1,file2
GID1A,input,1,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945046/GluePCA_GID1_input1_R1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945046/GluePCA_GID1_input1_R2.fastq.gz
GID1A,input,2,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945047/GluePCA_GID1_input2_R1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945047/GluePCA_GID1_input2_R2.fastq.gz
GID1A,input,3,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945048/GluePCA_GID1_input3_R1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945048/GluePCA_GID1_input3_R2.fastq.gz
GID1A,output,1,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945049/GluePCA_GID1_output1_2500uM_R1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945049/GluePCA_GID1_output1_2500uM_R2.fastq.gz
GID1A,output,2,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945050/GluePCA_GID1_output2_2500uM_R1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945050/GluePCA_GID1_output2_2500uM_R2.fastq.gz
GID1A,output,3,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945051/GluePCA_GID1_output3_2500uM_R1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/run/ERR169/ERR16945051/GluePCA_GID1_output3_2500uM_R2.fastq.gz
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