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fix: move primer file location under workflow; this avoids file not being found in shared filesystems #665

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merged 18 commits into from
Oct 23, 2024
Merged

fix: move primer file location under workflow; this avoids file not being found in shared filesystems #665

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8856029
fix: move nCoV-2019.primer.bed under workflow/resources
huzuner Sep 3, 2024
bdfb3db
fix: fix path of primers in main config
huzuner Sep 3, 2024
476c18a
fix: fix primer path to be called internally
huzuner Sep 4, 2024
c760d6a
fix: fix same in previous commit in read_clipping.smk
huzuner Sep 4, 2024
3ff8a39
Merge branch 'master' into fix/fix-primer-file-usage
huzuner Sep 27, 2024
4992906
define a function for getting kracken input in common.smk
huzuner Oct 7, 2024
453f916
fix get_kracken_input()
huzuner Oct 7, 2024
101c2ea
use get_kracken_input in qc.smk
huzuner Oct 7, 2024
1f1098d
restore all changes
huzuner Oct 9, 2024
fc71176
refactor: move checking the primer file for URL into the script
huzuner Oct 9, 2024
350bbdb
chore: fmt
huzuner Oct 10, 2024
59270a6
Merge branch 'master' into fix/fix-primer-file-usage
huzuner Oct 17, 2024
44646dc
Merge branch 'master' into fix/fix-primer-file-usage
huzuner Oct 21, 2024
2244f94
fix: disable formatting temporarily
huzuner Oct 21, 2024
9bf9151
Update main.yml
johanneskoester Oct 23, 2024
6bda5ce
Update main.yml
johanneskoester Oct 23, 2024
efb01c2
fmt script
johanneskoester Oct 23, 2024
3ea9b5c
add missing key to artifact name
johanneskoester Oct 23, 2024
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218 changes: 218 additions & 0 deletions workflow/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 +
MN908947.3 3507 3531 nCoV-2019_11_RIGHT 1 -
MN908947.3 3460 3482 nCoV-2019_12_LEFT 2 +
MN908947.3 3826 3853 nCoV-2019_12_RIGHT 2 -
MN908947.3 3771 3795 nCoV-2019_13_LEFT 1 +
MN908947.3 4142 4164 nCoV-2019_13_RIGHT 1 -
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 +
MN908947.3 4995 5017 nCoV-2019_16_RIGHT 2 -
MN908947.3 4939 4966 nCoV-2019_17_LEFT 1 +
MN908947.3 5296 5321 nCoV-2019_17_RIGHT 1 -
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 -
MN908947.3 5563 5586 nCoV-2019_19_LEFT 1 +
MN908947.3 5932 5957 nCoV-2019_19_RIGHT 1 -
MN908947.3 5867 5894 nCoV-2019_20_LEFT 2 +
MN908947.3 6247 6272 nCoV-2019_20_RIGHT 2 -
MN908947.3 6167 6196 nCoV-2019_21_LEFT 1 +
MN908947.3 6168 6197 nCoV-2019_21_LEFT_alt2 1 +
MN908947.3 6528 6550 nCoV-2019_21_RIGHT 1 -
MN908947.3 6526 6548 nCoV-2019_21_RIGHT_alt0 1 -
MN908947.3 6466 6495 nCoV-2019_22_LEFT 2 +
MN908947.3 6846 6873 nCoV-2019_22_RIGHT 2 -
MN908947.3 6718 6745 nCoV-2019_23_LEFT 1 +
MN908947.3 7092 7117 nCoV-2019_23_RIGHT 1 -
MN908947.3 7035 7058 nCoV-2019_24_LEFT 2 +
MN908947.3 7389 7415 nCoV-2019_24_RIGHT 2 -
MN908947.3 7305 7332 nCoV-2019_25_LEFT 1 +
MN908947.3 7671 7694 nCoV-2019_25_RIGHT 1 -
MN908947.3 7626 7651 nCoV-2019_26_LEFT 2 +
MN908947.3 7997 8019 nCoV-2019_26_RIGHT 2 -
MN908947.3 7943 7968 nCoV-2019_27_LEFT 1 +
MN908947.3 8319 8341 nCoV-2019_27_RIGHT 1 -
MN908947.3 8249 8275 nCoV-2019_28_LEFT 2 +
MN908947.3 8635 8661 nCoV-2019_28_RIGHT 2 -
MN908947.3 8595 8619 nCoV-2019_29_LEFT 1 +
MN908947.3 8954 8983 nCoV-2019_29_RIGHT 1 -
MN908947.3 8888 8913 nCoV-2019_30_LEFT 2 +
MN908947.3 9245 9271 nCoV-2019_30_RIGHT 2 -
MN908947.3 9204 9226 nCoV-2019_31_LEFT 1 +
MN908947.3 9557 9585 nCoV-2019_31_RIGHT 1 -
MN908947.3 9477 9502 nCoV-2019_32_LEFT 2 +
MN908947.3 9834 9858 nCoV-2019_32_RIGHT 2 -
MN908947.3 9784 9806 nCoV-2019_33_LEFT 1 +
MN908947.3 10146 10171 nCoV-2019_33_RIGHT 1 -
MN908947.3 10076 10099 nCoV-2019_34_LEFT 2 +
MN908947.3 10437 10459 nCoV-2019_34_RIGHT 2 -
MN908947.3 10362 10384 nCoV-2019_35_LEFT 1 +
MN908947.3 10737 10763 nCoV-2019_35_RIGHT 1 -
MN908947.3 10666 10688 nCoV-2019_36_LEFT 2 +
MN908947.3 11048 11074 nCoV-2019_36_RIGHT 2 -
MN908947.3 10999 11022 nCoV-2019_37_LEFT 1 +
MN908947.3 11372 11394 nCoV-2019_37_RIGHT 1 -
MN908947.3 11306 11331 nCoV-2019_38_LEFT 2 +
MN908947.3 11668 11693 nCoV-2019_38_RIGHT 2 -
MN908947.3 11555 11584 nCoV-2019_39_LEFT 1 +
MN908947.3 11927 11949 nCoV-2019_39_RIGHT 1 -
MN908947.3 11863 11889 nCoV-2019_40_LEFT 2 +
MN908947.3 12234 12256 nCoV-2019_40_RIGHT 2 -
MN908947.3 12110 12133 nCoV-2019_41_LEFT 1 +
MN908947.3 12465 12490 nCoV-2019_41_RIGHT 1 -
MN908947.3 12417 12439 nCoV-2019_42_LEFT 2 +
MN908947.3 12779 12802 nCoV-2019_42_RIGHT 2 -
MN908947.3 12710 12732 nCoV-2019_43_LEFT 1 +
MN908947.3 13074 13096 nCoV-2019_43_RIGHT 1 -
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 -
MN908947.3 20172 20200 nCoV-2019_67_LEFT 1 +
MN908947.3 20542 20572 nCoV-2019_67_RIGHT 1 -
MN908947.3 20472 20496 nCoV-2019_68_LEFT 2 +
MN908947.3 20867 20890 nCoV-2019_68_RIGHT 2 -
MN908947.3 20786 20813 nCoV-2019_69_LEFT 1 +
MN908947.3 21146 21169 nCoV-2019_69_RIGHT 1 -
MN908947.3 21075 21104 nCoV-2019_70_LEFT 2 +
MN908947.3 21427 21455 nCoV-2019_70_RIGHT 2 -
MN908947.3 21357 21386 nCoV-2019_71_LEFT 1 +
MN908947.3 21716 21743 nCoV-2019_71_RIGHT 1 -
MN908947.3 21658 21682 nCoV-2019_72_LEFT 2 +
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 -
MN908947.3 22262 22290 nCoV-2019_74_LEFT 2 +
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 workflow/rules/long_read.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ rule nanofilt:

rule downsample_and_trim_raw:
input:
primer=config["preprocessing"]["amplicon-primers"],
primer=workflow.source_path("../resources/nCoV-2019.primer.bed"),
reads="results/{date}/filtered/nanofilt/{sample}.fastq",
ref_genome="resources/genomes/main.fasta",
output:
Expand Down Expand Up @@ -121,7 +121,7 @@ rule canu_correct:

rule clip_adbc_corrected:
input:
primer=config["preprocessing"]["amplicon-primers"],
primer=workflow.source_path("../resources/nCoV-2019.primer.bed"),
reads="results/{date}/corrected/{sample}/{sample}.correctedReads.fasta",
ref_genome="resources/genomes/main.fasta",
output:
Expand Down
2 changes: 1 addition & 1 deletion workflow/rules/read_clipping.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ rule samtools_sort:

rule bed_to_bedpe:
input:
check_bed_for_URL(config["preprocessing"]["amplicon-primers"]),
check_bed_for_URL(workflow.source_path("../resources/nCoV-2019.primer.bed")),
output:
"resources/primer.bedpe",
log:
Expand Down
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