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feat: simplify csv files #263

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Jun 1, 2021
Merged

feat: simplify csv files #263

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14 changes: 7 additions & 7 deletions testdata/csv/tiny-manta-normal-https.csv
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
patient,gender,status,sample,lane,fastq1,fastq2
1234,XX,0,1234N,1234N_M1,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M2,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M4,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M5,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M6,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M7,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
patient,sample,lane,fastq1,fastq2
1234,1234N,1234N_M1,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M2,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M4,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M5,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M6,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M7,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
14 changes: 7 additions & 7 deletions testdata/csv/tiny-manta-normal.csv
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
patient,gender,status,sample,lane,fastq1,fastq2
1234,XX,0,1234N,1234N_M1,data/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M2,data/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M4,data/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M5,data/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M6,data/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
1234,XX,0,1234N,1234N_M7,data/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
patient,sample,lane,fastq1,fastq2
1234,1234N,1234N_M1,data/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M2,data/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M4,data/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M5,data/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M6,data/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
1234,1234N,1234N_M7,data/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz,data/testdata/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
4 changes: 2 additions & 2 deletions testdata/csv/tiny-recal-normal-https.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
patient,gender,status,sample,bam,bai
1234,XX,0,1234N,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/recalbam/1234N.recal.bam,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/recalbam/1234N.recal.bai
patient,sample,bam,bai
1234,1234N,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/recalbam/1234N.recal.bam,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/recalbam/1234N.recal.bai
4 changes: 2 additions & 2 deletions testdata/csv/tiny-recal-normal.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
patient,gender,status,sample,bam,bai
1234,XX,0,1234N,data/testdata/recalbam/1234N.recal.bam,data/testdata/recalbam/1234N.recal.bai
patient,sample,bam,bai
1234,1234N,data/testdata/recalbam/1234N.recal.bam,data/testdata/recalbam/1234N.recal.bai
4 changes: 2 additions & 2 deletions testdata/csv/tiny-umi-qiaseq-https.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
patient,gender,status,sample,lane,fastq1,fastq2
SRR7545951-small,XX,0,1234N,SRR7545951,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/qiaseq/SRR7545951-small_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/qiaseq/SRR7545951-small_2.fastq.gz
patient,sample,lane,fastq1,fastq2
SRR7545951-small,1234N,SRR7545951,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/qiaseq/SRR7545951-small_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/qiaseq/SRR7545951-small_2.fastq.gz
4 changes: 2 additions & 2 deletions testdata/csv/tiny-umi-tso-https.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
patient,gender,status,sample,lane,fastq1,fastq2
HT1080-chr20,XX,0,1234N,HT1080,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/tso/HT1080-chr20_S16_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/tso/HT1080-chr20_S16_R2_001.fastq.gz
patient,sample,lane,fastq1,fastq2
HT1080-chr20,1234N,HT1080,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/tso/HT1080-chr20_S16_R1_001.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/umi-dna/tso/HT1080-chr20_S16_R2_001.fastq.gz