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Update benchmarking TSV to eager3 format. update readme #1743

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Update benchmarking TSV to eager3 format. update readme #1743

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2508edf
Update benchmarking TSV to eager3 format. update readme
TCLamnidis Sep 19, 2025
8e137c4
fix pairment
TCLamnidis Sep 19, 2025
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4 changes: 3 additions & 1 deletion README.md
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Expand Up @@ -57,7 +57,9 @@ TSV input versions of BAM files exists for all files below.

#### Benchmarking

There are three test TSV input files that can be used for larger, more 'realistic' shotgun testing with full sized data. This currently covers three main contexts.
There are three test TSV input files that can be used for larger, more 'realistic' shotgun testing with full sized data.
This currently covers three main contexts.
Versions of these TSV files also exist in the new TSV format accepted by nf-core/eager 3+, and are prefixed with `eager3_`.

`benchmarking_human.tsv`: Ancient Fish from [Star et al. 2017](https://doi.org/10.1073/pnas.1710186114)
`benchmarking_vikingfish.tsv`: Ancient Humans from [Gamba et al. 2014](https://doi.org/10.1073/10.1038/ncomms6257)
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4 changes: 4 additions & 0 deletions testdata/Benchmarking/eager3_benchmarking_human.tsv
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sample_id library_id lane colour_chemistry pairment strandedness damage_treatment r1 r2 bam bam_reference_id
BR1 BR1 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187907/SRR1187907.fastq.gz
NE5 NE5 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187897/SRR1187897.fastq.gz
NE7 NE7 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/002/SRR1187902/SRR1187902.fastq.gz
12 changes: 12 additions & 0 deletions testdata/Benchmarking/eager3_benchmarking_pathogenscreening.tsv
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sample_id library_id lane colour_chemistry pairment strandedness damage_treatment r1 r2 bam bam_reference_id
KunilaII KunilaII_nonUDG 4 4 paired double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/007/ERR2112547/ERR2112547_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/007/ERR2112547/ERR2112547_2.fastq.gz
KunilaII KunilaII_UDG 4 4 paired double full ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/008/ERR2112548/ERR2112548_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/008/ERR2112548/ERR2112548_2.fastq.gz
6Post 6Post_PE 1 2 paired double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/009/ERR2112549/ERR2112549_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/009/ERR2112549/ERR2112549_2.fastq.gz
6Post 6Post_PE 2 2 paired double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/000/ERR2112550/ERR2112550_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/000/ERR2112550/ERR2112550_2.fastq.gz
6Post 6Post_PE 3 2 paired double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/001/ERR2112551/ERR2112551_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/001/ERR2112551/ERR2112551_2.fastq.gz
6Post 6Post_PE 4 2 paired double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/002/ERR2112552/ERR2112552_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/002/ERR2112552/ERR2112552_2.fastq.gz
6Post 6Post_SE 1 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/009/ERR2112569/ERR2112569.fastq.gz
6Post 6Post_SE 2 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/000/ERR2112570/ERR2112570.fastq.gz
6Post 6Post_SE 3 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/001/ERR2112571/ERR2112571.fastq.gz
6Post 6Post_SE 4 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/002/ERR2112572/ERR2112572.fastq.gz
6Post 6Post_SE 8 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/003/ERR2112573/ERR2112573.fastq.gz
7 changes: 7 additions & 0 deletions testdata/Benchmarking/eager3_benchmarking_vikingfish.tsv
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sample_id library_id lane colour_chemistry pairment strandedness damage_treatment r1 r2 bam bam_reference_id
COD076 COD076E1bL1 8 4 paired double none s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943600_1.fastq.gz s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943600_2.fastq.gz
COD076 COD076E1bL1 6 4 paired double none s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943601_1.fastq.gz s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943601_2.fastq.gz
COD076 COD076E1bL1 1 4 paired double none s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943602_1.fastq.gz s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943602_2.fastq.gz
COD092 COD092E1bL1i69 6 4 paired double none s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943607_1.fastq.gz s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943607_2.fastq.gz
COD092 COD092E1bL1i69 7 4 paired double none s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943608_1.fastq.gz s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943608_2.fastq.gz
COD092 COD092E1bL1i69 8 4 paired double none s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943609_1.fastq.gz s3://nf-core-awsmegatests/eager/ENA_Data_Fish/ERR1943609_2.fastq.gz