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TCLamnidisTCLamnidis
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fix pairment
1 parent 2508edf commit 8e137c4

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-20
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3 files changed

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‎testdata/Benchmarking/eager3_benchmarking_human.tsv‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
sample_id library_id lane colour_chemistry pairment strandedness damage_treatment r1 r2 bam bam_reference_id
2-
BR1 BR1 0 4 SE double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187907/SRR1187907.fastq.gz
3-
NE5 NE5 0 4 SE double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187897/SRR1187897.fastq.gz
4-
NE7 NE7 0 4 SE double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/002/SRR1187902/SRR1187902.fastq.gz
2+
BR1 BR1 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187907/SRR1187907.fastq.gz
3+
NE5 NE5 0 4 single double none ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/007/SRR1187897/SRR1187897.fastq.gz
4+
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

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,12 @@
11
sample_id library_id lane colour_chemistry pairment strandedness damage_treatment r1 r2 bam bam_reference_id
2-
KunilaII KunilaII_nonUDG 4 4 PE 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
3-
KunilaII KunilaII_UDG 4 4 PE 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
4-
6Post 6Post_PE 1 2 PE 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
5-
6Post 6Post_PE 2 2 PE 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
6-
6Post 6Post_PE 3 2 PE 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
7-
6Post 6Post_PE 4 2 PE 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
8-
6Post 6Post_SE 1 4 SE double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/009/ERR2112569/ERR2112569.fastq.gz
9-
6Post 6Post_SE 2 4 SE double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/000/ERR2112570/ERR2112570.fastq.gz
10-
6Post 6Post_SE 3 4 SE double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/001/ERR2112571/ERR2112571.fastq.gz
11-
6Post 6Post_SE 4 4 SE double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/002/ERR2112572/ERR2112572.fastq.gz
12-
6Post 6Post_SE 8 4 SE double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/003/ERR2112573/ERR2112573.fastq.gz
2+
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
3+
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
4+
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
5+
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
6+
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
7+
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
8+
6Post 6Post_SE 1 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/009/ERR2112569/ERR2112569.fastq.gz
9+
6Post 6Post_SE 2 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/000/ERR2112570/ERR2112570.fastq.gz
10+
6Post 6Post_SE 3 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/001/ERR2112571/ERR2112571.fastq.gz
11+
6Post 6Post_SE 4 4 single double half ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR211/002/ERR2112572/ERR2112572.fastq.gz
12+
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

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
sample_id library_id lane colour_chemistry pairment strandedness damage_treatment r1 r2 bam bam_reference_id
2-
COD076 COD076E1bL1 8 4 PE 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
3-
COD076 COD076E1bL1 6 4 PE 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
4-
COD076 COD076E1bL1 1 4 PE 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
5-
COD092 COD092E1bL1i69 6 4 PE 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
6-
COD092 COD092E1bL1i69 7 4 PE 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
7-
COD092 COD092E1bL1i69 8 4 PE 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
2+
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
3+
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
4+
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
5+
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
6+
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
7+
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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