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feat: rule and script bed_to_bedpe #447

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merged 11 commits into from
Feb 2, 2022
Merged

feat: rule and script bed_to_bedpe #447

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08df837
Rule and script bed_to_bedpe
AKBrueggemann Jan 11, 2022
e7e9408
Merge branch 'master' into bed-to-bedpe-file
AKBrueggemann Jan 11, 2022
6d7f116
Added bed to config, changed rule input paths
AKBrueggemann Jan 14, 2022
6ad3bde
Merge branch 'bed-to-bedpe-file' of https://github.com/IKIM-Essen/unc…
AKBrueggemann Jan 14, 2022
e7adb5d
Merge branch 'master' into bed-to-bedpe-file
AKBrueggemann Jan 14, 2022
25b97ba
Merge branch 'master' into bed-to-bedpe-file
AKBrueggemann Jan 18, 2022
1fe5e95
Bed files can be downloaded via url in config
AKBrueggemann Jan 28, 2022
794a6cd
Merge branch 'master' into bed-to-bedpe-file
AKBrueggemann Jan 28, 2022
34a0df7
fmt
AKBrueggemann Jan 28, 2022
049dce2
Merge branch 'bed-to-bedpe-file' of https://github.com/IKIM-Essen/unc…
AKBrueggemann Jan 28, 2022
30660e2
Merge branch 'master' into bed-to-bedpe-file
AKBrueggemann Jan 31, 2022
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2 changes: 1 addition & 1 deletion .tests/config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ preprocessing:
# for more information
artic-primer-version: 3
# path to amplicon primers in bedpe format for hard-clipping on paired end files (illumina)
amplicon-primers: "resources/primer.bedpe"
amplicon-primers: "resources/nCoV-2019.primer.bed"
# GenBank accession of reference sequence of the amplicon primers
amplicon-reference: "MN908947"

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218 changes: 218 additions & 0 deletions .tests/resources/nCoV-2019.primer.bed
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MN908947.3 30 54 nCoV-2019_1_LEFT 1 +
MN908947.3 385 410 nCoV-2019_1_RIGHT 1 -
MN908947.3 320 342 nCoV-2019_2_LEFT 2 +
MN908947.3 704 726 nCoV-2019_2_RIGHT 2 -
MN908947.3 642 664 nCoV-2019_3_LEFT 1 +
MN908947.3 1004 1028 nCoV-2019_3_RIGHT 1 -
MN908947.3 943 965 nCoV-2019_4_LEFT 2 +
MN908947.3 1312 1337 nCoV-2019_4_RIGHT 2 -
MN908947.3 1242 1264 nCoV-2019_5_LEFT 1 +
MN908947.3 1623 1651 nCoV-2019_5_RIGHT 1 -
MN908947.3 1573 1595 nCoV-2019_6_LEFT 2 +
MN908947.3 1942 1964 nCoV-2019_6_RIGHT 2 -
MN908947.3 1875 1897 nCoV-2019_7_LEFT 1 +
MN908947.3 1868 1890 nCoV-2019_7_LEFT_alt0 1 +
MN908947.3 2247 2269 nCoV-2019_7_RIGHT 1 -
MN908947.3 2242 2264 nCoV-2019_7_RIGHT_alt5 1 -
MN908947.3 2181 2205 nCoV-2019_8_LEFT 2 +
MN908947.3 2568 2592 nCoV-2019_8_RIGHT 2 -
MN908947.3 2505 2529 nCoV-2019_9_LEFT 1 +
MN908947.3 2504 2528 nCoV-2019_9_LEFT_alt4 1 +
MN908947.3 2882 2904 nCoV-2019_9_RIGHT 1 -
MN908947.3 2880 2902 nCoV-2019_9_RIGHT_alt2 1 -
MN908947.3 2826 2850 nCoV-2019_10_LEFT 2 +
MN908947.3 3183 3210 nCoV-2019_10_RIGHT 2 -
MN908947.3 3144 3166 nCoV-2019_11_LEFT 1 +
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MN908947.3 3460 3482 nCoV-2019_12_LEFT 2 +
MN908947.3 3826 3853 nCoV-2019_12_RIGHT 2 -
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MN908947.3 4054 4077 nCoV-2019_14_LEFT 2 +
MN908947.3 4044 4068 nCoV-2019_14_LEFT_alt4 2 +
MN908947.3 4428 4450 nCoV-2019_14_RIGHT 2 -
MN908947.3 4402 4424 nCoV-2019_14_RIGHT_alt2 2 -
MN908947.3 4294 4321 nCoV-2019_15_LEFT 1 +
MN908947.3 4296 4322 nCoV-2019_15_LEFT_alt1 1 +
MN908947.3 4674 4696 nCoV-2019_15_RIGHT 1 -
MN908947.3 4666 4689 nCoV-2019_15_RIGHT_alt3 1 -
MN908947.3 4636 4658 nCoV-2019_16_LEFT 2 +
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MN908947.3 4939 4966 nCoV-2019_17_LEFT 1 +
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MN908947.3 5230 5259 nCoV-2019_18_LEFT 2 +
MN908947.3 5257 5287 nCoV-2019_18_LEFT_alt2 2 +
MN908947.3 5620 5644 nCoV-2019_18_RIGHT 2 -
MN908947.3 5620 5643 nCoV-2019_18_RIGHT_alt1 2 -
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MN908947.3 5932 5957 nCoV-2019_19_RIGHT 1 -
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MN908947.3 6168 6197 nCoV-2019_21_LEFT_alt2 1 +
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MN908947.3 6526 6548 nCoV-2019_21_RIGHT_alt0 1 -
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MN908947.3 13005 13027 nCoV-2019_44_LEFT 2 +
MN908947.3 13007 13029 nCoV-2019_44_LEFT_alt3 2 +
MN908947.3 13378 13400 nCoV-2019_44_RIGHT 2 -
MN908947.3 13363 13385 nCoV-2019_44_RIGHT_alt0 2 -
MN908947.3 13319 13344 nCoV-2019_45_LEFT 1 +
MN908947.3 13307 13336 nCoV-2019_45_LEFT_alt2 1 +
MN908947.3 13669 13699 nCoV-2019_45_RIGHT 1 -
MN908947.3 13660 13689 nCoV-2019_45_RIGHT_alt7 1 -
MN908947.3 13599 13621 nCoV-2019_46_LEFT 2 +
MN908947.3 13602 13625 nCoV-2019_46_LEFT_alt1 2 +
MN908947.3 13962 13984 nCoV-2019_46_RIGHT 2 -
MN908947.3 13961 13984 nCoV-2019_46_RIGHT_alt2 2 -
MN908947.3 13918 13946 nCoV-2019_47_LEFT 1 +
MN908947.3 14271 14299 nCoV-2019_47_RIGHT 1 -
MN908947.3 14207 14232 nCoV-2019_48_LEFT 2 +
MN908947.3 14579 14601 nCoV-2019_48_RIGHT 2 -
MN908947.3 14545 14570 nCoV-2019_49_LEFT 1 +
MN908947.3 14898 14926 nCoV-2019_49_RIGHT 1 -
MN908947.3 14865 14895 nCoV-2019_50_LEFT 2 +
MN908947.3 15224 15246 nCoV-2019_50_RIGHT 2 -
MN908947.3 15171 15193 nCoV-2019_51_LEFT 1 +
MN908947.3 15538 15560 nCoV-2019_51_RIGHT 1 -
MN908947.3 15481 15503 nCoV-2019_52_LEFT 2 +
MN908947.3 15861 15886 nCoV-2019_52_RIGHT 2 -
MN908947.3 15827 15851 nCoV-2019_53_LEFT 1 +
MN908947.3 16186 16209 nCoV-2019_53_RIGHT 1 -
MN908947.3 16118 16144 nCoV-2019_54_LEFT 2 +
MN908947.3 16485 16510 nCoV-2019_54_RIGHT 2 -
MN908947.3 16416 16444 nCoV-2019_55_LEFT 1 +
MN908947.3 16804 16833 nCoV-2019_55_RIGHT 1 -
MN908947.3 16748 16770 nCoV-2019_56_LEFT 2 +
MN908947.3 17130 17152 nCoV-2019_56_RIGHT 2 -
MN908947.3 17065 17087 nCoV-2019_57_LEFT 1 +
MN908947.3 17430 17452 nCoV-2019_57_RIGHT 1 -
MN908947.3 17381 17406 nCoV-2019_58_LEFT 2 +
MN908947.3 17738 17761 nCoV-2019_58_RIGHT 2 -
MN908947.3 17674 17697 nCoV-2019_59_LEFT 1 +
MN908947.3 18036 18062 nCoV-2019_59_RIGHT 1 -
MN908947.3 17966 17993 nCoV-2019_60_LEFT 2 +
MN908947.3 18324 18348 nCoV-2019_60_RIGHT 2 -
MN908947.3 18253 18275 nCoV-2019_61_LEFT 1 +
MN908947.3 18650 18672 nCoV-2019_61_RIGHT 1 -
MN908947.3 18596 18618 nCoV-2019_62_LEFT 2 +
MN908947.3 18957 18979 nCoV-2019_62_RIGHT 2 -
MN908947.3 18896 18918 nCoV-2019_63_LEFT 1 +
MN908947.3 19275 19297 nCoV-2019_63_RIGHT 1 -
MN908947.3 19204 19232 nCoV-2019_64_LEFT 2 +
MN908947.3 19591 19616 nCoV-2019_64_RIGHT 2 -
MN908947.3 19548 19570 nCoV-2019_65_LEFT 1 +
MN908947.3 19911 19939 nCoV-2019_65_RIGHT 1 -
MN908947.3 19844 19866 nCoV-2019_66_LEFT 2 +
MN908947.3 20231 20255 nCoV-2019_66_RIGHT 2 -
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MN908947.3 20542 20572 nCoV-2019_67_RIGHT 1 -
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MN908947.3 21357 21386 nCoV-2019_71_LEFT 1 +
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MN908947.3 22013 22038 nCoV-2019_72_RIGHT 2 -
MN908947.3 21961 21990 nCoV-2019_73_LEFT 1 +
MN908947.3 22324 22346 nCoV-2019_73_RIGHT 1 -
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MN908947.3 22626 22650 nCoV-2019_74_RIGHT 2 -
MN908947.3 22516 22542 nCoV-2019_75_LEFT 1 +
MN908947.3 22877 22903 nCoV-2019_75_RIGHT 1 -
MN908947.3 22797 22819 nCoV-2019_76_LEFT 2 +
MN908947.3 22798 22821 nCoV-2019_76_LEFT_alt3 2 +
MN908947.3 23192 23214 nCoV-2019_76_RIGHT 2 -
MN908947.3 23189 23212 nCoV-2019_76_RIGHT_alt0 2 -
MN908947.3 23122 23144 nCoV-2019_77_LEFT 1 +
MN908947.3 23500 23522 nCoV-2019_77_RIGHT 1 -
MN908947.3 23443 23466 nCoV-2019_78_LEFT 2 +
MN908947.3 23822 23847 nCoV-2019_78_RIGHT 2 -
MN908947.3 23789 23812 nCoV-2019_79_LEFT 1 +
MN908947.3 24145 24169 nCoV-2019_79_RIGHT 1 -
MN908947.3 24078 24100 nCoV-2019_80_LEFT 2 +
MN908947.3 24443 24467 nCoV-2019_80_RIGHT 2 -
MN908947.3 24391 24416 nCoV-2019_81_LEFT 1 +
MN908947.3 24765 24789 nCoV-2019_81_RIGHT 1 -
MN908947.3 24696 24721 nCoV-2019_82_LEFT 2 +
MN908947.3 25052 25076 nCoV-2019_82_RIGHT 2 -
MN908947.3 24978 25003 nCoV-2019_83_LEFT 1 +
MN908947.3 25347 25369 nCoV-2019_83_RIGHT 1 -
MN908947.3 25279 25301 nCoV-2019_84_LEFT 2 +
MN908947.3 25646 25673 nCoV-2019_84_RIGHT 2 -
MN908947.3 25601 25623 nCoV-2019_85_LEFT 1 +
MN908947.3 25969 25994 nCoV-2019_85_RIGHT 1 -
MN908947.3 25902 25924 nCoV-2019_86_LEFT 2 +
MN908947.3 26290 26315 nCoV-2019_86_RIGHT 2 -
MN908947.3 26197 26219 nCoV-2019_87_LEFT 1 +
MN908947.3 26566 26590 nCoV-2019_87_RIGHT 1 -
MN908947.3 26520 26542 nCoV-2019_88_LEFT 2 +
MN908947.3 26890 26913 nCoV-2019_88_RIGHT 2 -
MN908947.3 26835 26857 nCoV-2019_89_LEFT 1 +
MN908947.3 26838 26860 nCoV-2019_89_LEFT_alt2 1 +
MN908947.3 27202 27227 nCoV-2019_89_RIGHT 1 -
MN908947.3 27190 27215 nCoV-2019_89_RIGHT_alt4 1 -
MN908947.3 27141 27164 nCoV-2019_90_LEFT 2 +
MN908947.3 27511 27533 nCoV-2019_90_RIGHT 2 -
MN908947.3 27446 27471 nCoV-2019_91_LEFT 1 +
MN908947.3 27825 27854 nCoV-2019_91_RIGHT 1 -
MN908947.3 27784 27808 nCoV-2019_92_LEFT 2 +
MN908947.3 28145 28172 nCoV-2019_92_RIGHT 2 -
MN908947.3 28081 28104 nCoV-2019_93_LEFT 1 +
MN908947.3 28442 28464 nCoV-2019_93_RIGHT 1 -
MN908947.3 28394 28416 nCoV-2019_94_LEFT 2 +
MN908947.3 28756 28779 nCoV-2019_94_RIGHT 2 -
MN908947.3 28677 28699 nCoV-2019_95_LEFT 1 +
MN908947.3 29041 29063 nCoV-2019_95_RIGHT 1 -
MN908947.3 28985 29007 nCoV-2019_96_LEFT 2 +
MN908947.3 29356 29378 nCoV-2019_96_RIGHT 2 -
MN908947.3 29288 29316 nCoV-2019_97_LEFT 1 +
MN908947.3 29665 29693 nCoV-2019_97_RIGHT 1 -
MN908947.3 29486 29510 nCoV-2019_98_LEFT 2 +
MN908947.3 29836 29866 nCoV-2019_98_RIGHT 2 -
4 changes: 2 additions & 2 deletions config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,8 @@ preprocessing:
# https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4
# for more information
artic-primer-version: 3
# path to amplicon primers in bedpe format for hard-clipping on paired end files (illumina)
amplicon-primers: "resources/primer.bedpe"
# path to amplicon primers in bed format for hard-clipping on paired end files (illumina) or url to file that should be downloaded
amplicon-primers: "resources/nCoV-2019.primer.bed"
# GenBank accession of reference sequence of the amplicon primers
amplicon-reference: "MN908947"

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