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modifications for awsbatch #8

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Nov 1, 2018
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modifications for awsbatch #8

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22 changes: 11 additions & 11 deletions testdata/tsv/tiny-manta-s3.tsv
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
1234 XX 0 1234N 1234N_M1 s3://caw-test-data/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz s3://caw-test-data/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M2 s3://caw-test-data/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz s3://caw-test-data/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M4 s3://caw-test-data/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz s3://caw-test-data/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M5 s3://caw-test-data/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz s3://caw-test-data/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M6 s3://caw-test-data/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz s3://caw-test-data/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M7 s3://caw-test-data/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz s3://caw-test-data/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M1 s3://caw-test-data/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz s3://caw-test-data/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M2 s3://caw-test-data/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz s3://caw-test-data/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M3 s3://caw-test-data/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz s3://caw-test-data/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M4 s3://caw-test-data/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz s3://caw-test-data/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M5 s3://caw-test-data/manta/tumor/C09D_T_111207.8.ACCAACTG_R1_xxx.fastq.gz s3://caw-test-data/manta/tumor/C09D_T_111207.8.ACCAACTG_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M1 s3://sarek-tiny-test/manta/normal/C097F_N_111207.1.AGTTGCTT_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/normal/C097F_N_111207.1.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M2 s3://sarek-tiny-test/manta/normal/C097F_N_111207.2.AGTTGCTT_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/normal/C097F_N_111207.2.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M4 s3://sarek-tiny-test/manta/normal/C09DF_N_111207.4.AGTTGCTT_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/normal/C09DF_N_111207.4.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M5 s3://sarek-tiny-test/manta/normal/D0F23_N_111212.1.AGTTGCTT_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/normal/D0F23_N_111212.1.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M6 s3://sarek-tiny-test/manta/normal/D0F23_N_111212.2.AGTTGCTT_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/normal/D0F23_N_111212.2.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_M7 s3://sarek-tiny-test/manta/normal/D0F23_N_111212.3.AGTTGCTT_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/normal/D0F23_N_111212.3.AGTTGCTT_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M1 s3://sarek-tiny-test/manta/tumor/C09D_T_111207.3.ACCAACTG_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/tumor/C09D_T_111207.3.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M2 s3://sarek-tiny-test/manta/tumor/C09D_T_111207.5.ACCAACTG_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/tumor/C09D_T_111207.5.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M3 s3://sarek-tiny-test/manta/tumor/C09D_T_111207.6.ACCAACTG_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/tumor/C09D_T_111207.6.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M4 s3://sarek-tiny-test/manta/tumor/C09D_T_111207.7.ACCAACTG_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/tumor/C09D_T_111207.7.ACCAACTG_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_M5 s3://sarek-tiny-test/manta/tumor/C09D_T_111207.8.ACCAACTG_R1_xxx.fastq.gz s3://sarek-tiny-test/manta/tumor/C09D_T_111207.8.ACCAACTG_R2_xxx.fastq.gz
26 changes: 13 additions & 13 deletions testdata/tsv/tiny-s3.tsv
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
1234 XX 0 1234N 1234N_1 s3://caw-test-data/tiny/normal/tiny_n_L001_R1_xxx.fastq.gz s3://caw-test-data/tiny/normal/tiny_n_L001_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_2 s3://caw-test-data/tiny/normal/tiny_n_L002_R1_xxx.fastq.gz s3://caw-test-data/tiny/normal/tiny_n_L002_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_4 s3://caw-test-data/tiny/normal/tiny_n_L004_R1_xxx.fastq.gz s3://caw-test-data/tiny/normal/tiny_n_L004_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_7 s3://caw-test-data/tiny/normal/tiny_n_L007_R1_xxx.fastq.gz s3://caw-test-data/tiny/normal/tiny_n_L007_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_8 s3://caw-test-data/tiny/normal/tiny_n_L008_R1_xxx.fastq.gz s3://caw-test-data/tiny/normal/tiny_n_L008_R2_xxx.fastq.gz
1234 XX 0 1234N DUMMY_N s3://caw-test-data/dummy/normal/dummy_n_R1_xxx.fastq.gz s3://caw-test-data/dummy/normal/dummy_n_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_1 s3://caw-test-data/tiny/tumor/tiny_t_L001_R1_xxx.fastq.gz s3://caw-test-data/tiny/tumor/tiny_t_L001_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_2 s3://caw-test-data/tiny/tumor/tiny_t_L002_R1_xxx.fastq.gz s3://caw-test-data/tiny/tumor/tiny_t_L002_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_3 s3://caw-test-data/tiny/tumor/tiny_t_L003_R1_xxx.fastq.gz s3://caw-test-data/tiny/tumor/tiny_t_L003_R2_xxx.fastq.gz
1234 XX 1 9876T DUMMY_T s3://caw-test-data/dummy/tumor/dummy_t_R1_xxx.fastq.gz s3://caw-test-data/dummy/tumor/dummy_t_R2_xxx.fastq.gz
1234 XX 1 9877R 9877R_5 s3://caw-test-data/tiny/tumor/tiny_t_L005_R1_xxx.fastq.gz s3://caw-test-data/tiny/tumor/tiny_t_L005_R2_xxx.fastq.gz
1234 XX 1 9877R 9877R_6 s3://caw-test-data/tiny/tumor/tiny_t_L006_R1_xxx.fastq.gz s3://caw-test-data/tiny/tumor/tiny_t_L006_R2_xxx.fastq.gz
1234 XX 1 9877R 9877R_7 s3://caw-test-data/tiny/tumor/tiny_t_L007_R1_xxx.fastq.gz s3://caw-test-data/tiny/tumor/tiny_t_L007_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_1 s3://sarek-tiny-test/tiny/normal/tiny_n_L001_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/normal/tiny_n_L001_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_2 s3://sarek-tiny-test/tiny/normal/tiny_n_L002_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/normal/tiny_n_L002_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_4 s3://sarek-tiny-test/tiny/normal/tiny_n_L004_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/normal/tiny_n_L004_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_7 s3://sarek-tiny-test/tiny/normal/tiny_n_L007_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/normal/tiny_n_L007_R2_xxx.fastq.gz
1234 XX 0 1234N 1234N_8 s3://sarek-tiny-test/tiny/normal/tiny_n_L008_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/normal/tiny_n_L008_R2_xxx.fastq.gz
1234 XX 0 1234N DUMMY_N s3://sarek-tiny-test/dummy/normal/dummy_n_R1_xxx.fastq.gz s3://sarek-tiny-test/dummy/normal/dummy_n_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_1 s3://sarek-tiny-test/tiny/tumor/tiny_t_L001_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/tumor/tiny_t_L001_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_2 s3://sarek-tiny-test/tiny/tumor/tiny_t_L002_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/tumor/tiny_t_L002_R2_xxx.fastq.gz
1234 XX 1 9876T 9876T_3 s3://sarek-tiny-test/tiny/tumor/tiny_t_L003_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/tumor/tiny_t_L003_R2_xxx.fastq.gz
1234 XX 1 9876T DUMMY_T s3://sarek-tiny-test/dummy/tumor/dummy_t_R1_xxx.fastq.gz s3://sarek-tiny-test/dummy/tumor/dummy_t_R2_xxx.fastq.gz
1234 XX 1 9877R 9877R_5 s3://sarek-tiny-test/tiny/tumor/tiny_t_L005_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/tumor/tiny_t_L005_R2_xxx.fastq.gz
1234 XX 1 9877R 9877R_6 s3://sarek-tiny-test/tiny/tumor/tiny_t_L006_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/tumor/tiny_t_L006_R2_xxx.fastq.gz
1234 XX 1 9877R 9877R_7 s3://sarek-tiny-test/tiny/tumor/tiny_t_L007_R1_xxx.fastq.gz s3://sarek-tiny-test/tiny/tumor/tiny_t_L007_R2_xxx.fastq.gz