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Merge pull request #1743 from TCLamnidis/eager
Update benchmarking TSV to eager3 format. update readme
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‎README.md‎

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@@ -59,7 +59,9 @@ TSV input versions of BAM files exists for all files below.
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#### Benchmarking
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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.
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There are three test TSV input files that can be used for larger, more 'realistic' shotgun testing with full sized data.
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This currently covers three main contexts.
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Versions of these TSV files also exist in the new TSV format accepted by nf-core/eager 3+, and are prefixed with `eager3_`.
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`benchmarking_human.tsv`: Ancient Fish from [Star et al. 2017](https://doi.org/10.1073/pnas.1710186114)
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`benchmarking_vikingfish.tsv`: Ancient Humans from [Gamba et al. 2014](https://doi.org/10.1073/10.1038/ncomms6257)

‎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
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BR1 BR1 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187907/SRR1187907.fastq.gz
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NE5 NE5 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187897/SRR1187897.fastq.gz
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NE7 NE7 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/002/SRR1187902/SRR1187902.fastq.gz

‎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
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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
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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
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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
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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
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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
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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
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6Post 6Post_SE 1 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/009/ERR2112569/ERR2112569.fastq.gz
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6Post 6Post_SE 2 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/000/ERR2112570/ERR2112570.fastq.gz
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6Post 6Post_SE 3 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/001/ERR2112571/ERR2112571.fastq.gz
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6Post 6Post_SE 4 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/002/ERR2112572/ERR2112572.fastq.gz
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6Post 6Post_SE 8 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/003/ERR2112573/ERR2112573.fastq.gz

‎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
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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
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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
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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
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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
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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
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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

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