diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/.dockstore.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/.dockstore.yml new file mode 100644 index 0000000000..363c501606 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/.dockstore.yml @@ -0,0 +1,15 @@ +version: 1.2 +workflows: +- name: main + subclass: Galaxy + publish: true + primaryDescriptorPath: /SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac.ga + testParameterFiles: + - /SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac-tests.yml + authors: + - name: Polina Polunina + orcid: 0000-0002-0507-460 + - name: "B\xE9r\xE9nice Batut" + orcid: 0000-0001-9852-198 + - name: Wolfgang Maier + orcid: 0000-0002-9464-664 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/CHANGELOG.md new file mode 100644 index 0000000000..dd7aac8b6b --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/CHANGELOG.md @@ -0,0 +1,5 @@ +# Changelog + +## [0.1] + +- Initial version of COVID-19: variation analysis on ARTIC PE data workflow diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/README.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/README.md new file mode 100644 index 0000000000..04e94b582f --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/README.md @@ -0,0 +1,4 @@ +SARS-CoV-2 wastewater surveillance: lineages analysis on ARTIC PE data +--------------------------------------------- + +The workflow for SARS-CoV-2 wastewater Illumina-sequenced ARTIC data analysis diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac-tests.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac-tests.yml new file mode 100644 index 0000000000..e8bf17f232 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac-tests.yml @@ -0,0 +1,45 @@ +- doc: Test outline for SARS-CoV-2-wastewater-analysis-from-tiled-amplicon-PE-data-with-Freyja-and-Cojac + job: + ARTIC primer scheme: + class: File + path: test-data/primers.bed + filetype: bed + VCF: + class: Collection + collection_type: list + elements: + - 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a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_sample13.fastq.bam b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_sample13.fastq.bam new file mode 100644 index 0000000000..c1217213dd Binary files /dev/null and b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_sample13.fastq.bam differ diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/VCF_sample1.fastq.vcf b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/VCF_sample1.fastq.vcf new file mode 100644 index 0000000000..f4541fec13 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/VCF_sample1.fastq.vcf @@ -0,0 +1,137 @@ +##fileformat=VCFv4.0 +##fileDate=20221122 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-7475 -o /data/jwd01/main/052/596/52596651/tmp/lofreq2_call_parallel_8j0dt40/0.vcf.gz reads.bam +##reference=reference.fa +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 517 . TATG T 542 PASS DP=60;AF=0.316667;SB=0;DP4=21,20,9,10;INDEL;HRUN=1 +NC_045512.2 520 . GGTT G 54 PASS DP=60;AF=0.033333;SB=0;DP4=29,29,1,1;INDEL;HRUN=2 +NC_045512.2 761 . A G 168 PASS DP=27;AF=0.222222;SB=0;DP4=12,9,3,3 +NC_045512.2 2470 . C T 147 PASS DP=60;AF=0.100000;SB=0;DP4=20,34,2,4 +NC_045512.2 2832 . A G 703 PASS DP=47;AF=0.489362;SB=2;DP4=10,10,16,11 +NC_045512.2 2881 . C A 81 PASS DP=109;AF=0.036697;SB=0;DP4=67,37,3,1 +NC_045512.2 3037 . C T 8543 PASS DP=248;AF=0.939516;SB=0;DP4=0,0,122,126 +NC_045512.2 3039 . A G 87 PASS DP=246;AF=0.020325;SB=1;DP4=116,122,4,3 +NC_045512.2 3104 . T C 200 PASS DP=139;AF=0.064748;SB=1;DP4=53,75,3,7 +NC_045512.2 4181 . G T 229 PASS DP=68;AF=0.132353;SB=0;DP4=29,28,5,5 +NC_045512.2 5386 . T G 1661 PASS DP=62;AF=0.774194;SB=0;DP4=5,4,26,26 +NC_045512.2 5730 . C T 937 PASS DP=142;AF=0.239437;SB=0;DP4=53,52,18,19 +NC_045512.2 5812 . C T 361 PASS DP=142;AF=0.105634;SB=0;DP4=61,62,9,9 +NC_045512.2 6402 . C T 454 PASS DP=62;AF=0.258065;SB=0;DP4=22,22,9,9 +NC_045512.2 6512 . AGTT A 470 PASS DP=30;AF=0.533333;SB=1;DP4=8,6,7,9;INDEL;HRUN=1 +NC_045512.2 7124 . C T 175 PASS DP=22;AF=0.272727;SB=0;DP4=10,5,5,2 +NC_045512.2 7482 . C T 415 PASS DP=41;AF=0.341463;SB=0;DP4=14,12,8,6 +NC_045512.2 7851 . C T 199 PASS DP=68;AF=0.117647;SB=0;DP4=30,30,4,4 +NC_045512.2 8393 . G A 568 PASS DP=31;AF=0.548387;SB=0;DP4=7,3,14,7 +NC_045512.2 8808 . A G 170 PASS DP=68;AF=0.102941;SB=0;DP4=30,29,4,5 +NC_045512.2 8986 . C T 260 PASS DP=31;AF=0.290323;SB=5;DP4=12,9,8,2 +NC_045512.2 9053 . G T 439 PASS DP=46;AF=0.326087;SB=0;DP4=18,12,9,7 +NC_045512.2 9891 . C T 147 PASS DP=31;AF=0.193548;SB=0;DP4=14,10,4,3 +NC_045512.2 10029 . C T 1097 PASS DP=44;AF=0.727273;SB=0;DP4=5,5,17,17 +NC_045512.2 10135 . T C 76 PASS DP=28;AF=0.107143;SB=0;DP4=15,10,2,1 +NC_045512.2 10449 . C A 1166 PASS DP=41;AF=0.853659;SB=7;DP4=1,4,20,16 +NC_045512.2 11201 . A G 326 PASS DP=60;AF=0.200000;SB=0;DP4=23,23,7,7 +NC_045512.2 11282 . AGTTTGTCTG A 927 PASS DP=34;AF=0.735294;SB=0;DP4=5,6,11,14;INDEL;HRUN=1 +NC_045512.2 11332 . A G 76 PASS DP=27;AF=0.111111;SB=0;DP4=10,13,2,2 +NC_045512.2 11418 . T C 242 PASS DP=46;AF=0.195652;SB=0;DP4=21,16,5,4 +NC_045512.2 11514 . C T 442 PASS DP=72;AF=0.222222;SB=0;DP4=27,27,9,9 +NC_045512.2 11537 . A G 1099 PASS DP=72;AF=0.486111;SB=0;DP4=17,17,19,19 +NC_045512.2 13019 . C T 159 PASS DP=96;AF=0.072917;SB=0;DP4=44,45,4,3 +NC_045512.2 13195 . T C 1110 PASS DP=40;AF=0.825000;SB=1;DP4=4,2,18,16 +NC_045512.2 14408 . C T 1146 PASS DP=34;AF=0.911765;SB=0;DP4=0,0,20,14 +NC_045512.2 14889 . C T 93 PASS DP=60;AF=0.066667;SB=0;DP4=28,28,2,2 +NC_045512.2 15240 . C T 1229 PASS DP=45;AF=0.800000;SB=0;DP4=4,4,19,18 +NC_045512.2 15451 . G A 390 PASS DP=94;AF=0.159574;SB=0;DP4=38,38,9,9 +NC_045512.2 16466 . C T 153 PASS DP=38;AF=0.157895;SB=0;DP4=15,17,3,3 +NC_045512.2 18163 . A G 2007 PASS DP=79;AF=0.746835;SB=1;DP4=9,8,30,32 +NC_045512.2 18699 . T A 144 PASS DP=63;AF=0.095238;SB=0;DP4=29,28,3,3 +NC_045512.2 19089 . C T 83 PASS DP=100;AF=0.040000;SB=0;DP4=48,48,2,2 +NC_045512.2 19092 . T C 297 PASS DP=100;AF=0.120000;SB=0;DP4=44,44,6,6 +NC_045512.2 19220 . C T 74 PASS DP=32;AF=0.093750;SB=9;DP4=14,14,0,4 +NC_045512.2 20320 . C T 90 PASS DP=68;AF=0.058824;SB=0;DP4=31,32,2,2 +NC_045512.2 20369 . T C 67 PASS DP=55;AF=0.054545;SB=0;DP4=24,28,1,2 +NC_045512.2 21034 . C T 125 PASS DP=44;AF=0.113636;SB=4;DP4=21,18,4,1 +NC_045512.2 21618 . C G 421 PASS DP=60;AF=0.250000;SB=4;DP4=24,20,6,10 +NC_045512.2 21762 . C T 2028 PASS DP=70;AF=0.857143;SB=0;DP4=3,3,32,32 +NC_045512.2 21764 . ATACATG A 1935 PASS DP=70;AF=0.828571;SB=0;DP4=6,6,29,29;INDEL;HRUN=1 +NC_045512.2 21846 . C T 1215 PASS DP=35;AF=0.942857;SB=0;DP4=0,0,13,22 +NC_045512.2 21986 . GGTGTTTATT G 1506 PASS DP=69;AF=0.681159;SB=0;DP4=12,10,28,19;INDEL;HRUN=3 +NC_045512.2 22028 . GAGTTCA G 665 PASS DP=129;AF=0.170543;SB=0;DP4=54,53,11,11;INDEL;HRUN=1 +NC_045512.2 22193 . AATT A 1838 PASS DP=78;AF=0.769231;SB=2;DP4=11,12,25,35;INDEL;HRUN=2 +NC_045512.2 22204 . T TGAGCCAGAA 1392 PASS DP=75;AF=0.573333;SB=0;DP4=13,18,18,25;INDEL;HRUN=1 +NC_045512.2 22227 . C T 114 PASS DP=72;AF=0.069444;SB=0;DP4=29,38,2,3 +NC_045512.2 22578 . G A 1712 PASS DP=70;AF=0.714286;SB=0;DP4=8,8,27,27 +NC_045512.2 22599 . G A 197 PASS DP=70;AF=0.114286;SB=0;DP4=30,30,5,5 +NC_045512.2 22673 . T C 1094 PASS DP=53;AF=0.622642;SB=1;DP4=5,7,18,18 +NC_045512.2 22674 . C T 1023 PASS DP=53;AF=0.584906;SB=1;DP4=5,7,18,17 +NC_045512.2 22679 . T C 1329 PASS DP=56;AF=0.714286;SB=0;DP4=8,8,19,21 +NC_045512.2 22686 . C T 1336 PASS DP=51;AF=0.764706;SB=0;DP4=6,6,18,21 +NC_045512.2 22813 . G T 751 PASS DP=67;AF=0.388060;SB=2;DP4=22,18,17,10 +NC_045512.2 22882 . T G 2253 PASS DP=124;AF=0.564516;SB=0;DP4=25,25,38,35 +NC_045512.2 22898 . G A 2431 PASS DP=132;AF=0.568182;SB=0;DP4=25,25,41,41 +NC_045512.2 22917 . T G 1191 PASS DP=131;AF=0.312977;SB=0;DP4=41,41,24,25 +NC_045512.2 22992 . G A 2954 PASS DP=128;AF=0.687500;SB=4;DP4=15,19,51,43 +NC_045512.2 22995 . C A 4434 PASS DP=130;AF=0.938462;SB=0;DP4=0,0,66,64 +NC_045512.2 23013 . A C 2949 PASS DP=121;AF=0.735537;SB=2;DP4=11,15,48,47 +NC_045512.2 23040 . A G 2201 PASS DP=75;AF=0.826667;SB=1;DP4=3,5,34,33 +NC_045512.2 23048 . G A 2156 PASS DP=78;AF=0.782051;SB=1;DP4=4,6,33,35 +NC_045512.2 23055 . A G 1974 PASS DP=79;AF=0.708861;SB=3;DP4=3,6,31,31 +NC_045512.2 23063 . A T 2458 PASS DP=87;AF=0.804598;SB=4;DP4=4,8,37,38 +NC_045512.2 23075 . T C 2556 PASS DP=90;AF=0.822222;SB=1;DP4=5,7,40,38 +NC_045512.2 23202 . C A 2097 PASS DP=78;AF=0.794872;SB=0;DP4=6,6,32,34 +NC_045512.2 23403 . A G 1811 PASS DP=54;AF=0.907407;SB=0;DP4=0,0,27,26 +NC_045512.2 23525 . C T 807 PASS DP=30;AF=0.766667;SB=0;DP4=2,2,10,16 +NC_045512.2 23599 . T G 1072 PASS DP=44;AF=0.750000;SB=3;DP4=8,2,21,13 +NC_045512.2 23604 . C A 1198 PASS DP=49;AF=0.755102;SB=0;DP4=0,0,23,15 +NC_045512.2 23604 . C G 257 PASS DP=49;AF=0.224490;SB=0;DP4=0,0,8,3 +NC_045512.2 23663 . G T 82 PASS DP=104;AF=0.038462;SB=0;DP4=57,43,2,2 +NC_045512.2 23854 . C A 2171 PASS DP=87;AF=0.747126;SB=3;DP4=5,12,29,41 +NC_045512.2 23948 . G T 370 PASS DP=16;AF=0.687500;SB=2;DP4=2,2,8,4 +NC_045512.2 23996 . C T 102 PASS DP=31;AF=0.129032;SB=0;DP4=15,12,2,2 +NC_045512.2 24130 . C A 618 PASS DP=30;AF=0.633333;SB=1;DP4=4,6,10,10 +NC_045512.2 24410 . G A 563 PASS DP=58;AF=0.327586;SB=0;DP4=18,18,11,11 +NC_045512.2 24424 . A T 1058 PASS DP=56;AF=0.589286;SB=0;DP4=10,11,17,17 +NC_045512.2 24469 . T A 864 PASS DP=44;AF=0.659091;SB=1;DP4=7,8,16,13 +NC_045512.2 24503 . C T 1027 PASS DP=44;AF=0.704545;SB=7;DP4=5,8,19,12 +NC_045512.2 24803 . A G 137 PASS DP=26;AF=0.192308;SB=26;DP4=5,15,6,0 +NC_045512.2 25000 . C T 2820 PASS DP=100;AF=0.800000;SB=0;DP4=6,6,44,42 +NC_045512.2 25352 . G A 211 PASS DP=51;AF=0.156863;SB=1;DP4=15,26,4,5 +NC_045512.2 25469 . C T 698 PASS DP=116;AF=0.224138;SB=0;DP4=45,42,15,14 +NC_045512.2 25584 . C T 3212 PASS DP=138;AF=0.688406;SB=0;DP4=18,18,51,51 +NC_045512.2 25844 . C T 149 PASS DP=54;AF=0.111111;SB=0;DP4=24,24,3,3 +NC_045512.2 26078 . C T 189 PASS DP=39;AF=0.179487;SB=0;DP4=18,12,5,3 +NC_045512.2 26270 . C T 652 PASS DP=19;AF=0.947368;SB=0;DP4=0,1,4,14 +NC_045512.2 26530 . A G 2740 PASS DP=132;AF=0.628788;SB=0;DP4=15,17,41,47 +NC_045512.2 26577 . C G 1570 PASS DP=69;AF=0.695652;SB=1;DP4=8,11,19,31 +NC_045512.2 26709 . G A 3718 PASS DP=157;AF=0.707006;SB=0;DP4=18,14,68,55 +NC_045512.2 26767 . T C 1110 PASS DP=224;AF=0.187500;SB=0;DP4=87,88,24,24 +NC_045512.2 27259 . A C 1605 PASS DP=57;AF=0.824561;SB=0;DP4=4,3,28,22 +NC_045512.2 27638 . T C 578 PASS DP=66;AF=0.303030;SB=0;DP4=22,22,11,11 +NC_045512.2 27752 . C T 414 PASS DP=61;AF=0.245902;SB=0;DP4=22,22,8,9 +NC_045512.2 27807 . C T 1882 PASS DP=71;AF=0.788732;SB=1;DP4=5,7,30,29 +NC_045512.2 27874 . C T 140 PASS DP=76;AF=0.078947;SB=0;DP4=35,35,3,3 +NC_045512.2 28247 . AGATTTC A 907 PASS DP=100;AF=0.330000;SB=0;DP4=38,31,17,16;INDEL;HRUN=1 +NC_045512.2 28270 . TA T 939 PASS DP=96;AF=0.312500;SB=2;DP4=38,32,14,16;INDEL;HRUN=4 +NC_045512.2 28271 . A T 2011 PASS DP=96;AF=0.593750;SB=0;DP4=1,0,35,29 +NC_045512.2 28311 . C T 1845 PASS DP=88;AF=0.625000;SB=0;DP4=11,13,31,32 +NC_045512.2 28361 . GGAGAACGCA G 1970 PASS DP=72;AF=0.777778;SB=8;DP4=4,12,27,29;INDEL;HRUN=2 +NC_045512.2 28877 . A T 223 PASS DP=36;AF=0.222222;SB=3;DP4=15,12,7,2 +NC_045512.2 28878 . G C 222 PASS DP=35;AF=0.228571;SB=6;DP4=15,12,7,1 +NC_045512.2 28881 . G A 574 PASS DP=35;AF=0.542857;SB=0;DP4=0,0,14,7 +NC_045512.2 28881 . G T 392 PASS DP=35;AF=0.400000;SB=0;DP4=0,0,8,6 +NC_045512.2 28882 . G A 649 PASS DP=35;AF=0.600000;SB=1;DP4=8,6,14,7 +NC_045512.2 28883 . G C 634 PASS DP=36;AF=0.583333;SB=1;DP4=8,5,15,7 +NC_045512.2 28916 . G T 267 PASS DP=56;AF=0.178571;SB=0;DP4=28,17,6,4 +NC_045512.2 29301 . A G 133 PASS DP=96;AF=0.062500;SB=0;DP4=45,45,3,3 +NC_045512.2 29402 . G T 305 PASS DP=89;AF=0.134831;SB=1;DP4=33,39,8,7 +NC_045512.2 29422 . G T 115 PASS DP=69;AF=0.072464;SB=0;DP4=27,36,2,3 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/VCF_sample13.fastq.vcf b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/VCF_sample13.fastq.vcf new file mode 100644 index 0000000000..3033ee64e6 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/VCF_sample13.fastq.vcf @@ -0,0 +1,124 @@ +##fileformat=VCFv4.0 +##fileDate=20221122 +##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-7475 -o /data/jwd01/main/052/596/52596652/tmp/lofreq2_call_paralleleqsj2n37/0.vcf.gz reads.bam +##reference=reference.fa +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 210 . G T 850 PASS DP=25;AF=0.960000;SB=0;DP4=0,0,11,14 +NC_045512.2 241 . C T 554 PASS DP=16;AF=0.937500;SB=0;DP4=0,0,5,11 +NC_045512.2 1820 . G A 259 PASS DP=36;AF=0.250000;SB=0;DP4=10,16,4,6 +NC_045512.2 2832 . A G 283 PASS DP=69;AF=0.159420;SB=12;DP4=35,21,4,9 +NC_045512.2 3037 . C T 10693 PASS DP=328;AF=0.914634;SB=0;DP4=0,0,147,181 +NC_045512.2 3039 . A G 1108 PASS DP=323;AF=0.139319;SB=0;DP4=123,151,22,27 +NC_045512.2 3259 . G T 199 PASS DP=136;AF=0.066176;SB=0;DP4=61,66,4,5 +NC_045512.2 4181 . G T 1034 PASS DP=50;AF=0.620000;SB=4;DP4=5,10,18,17 +NC_045512.2 4320 . C T 69 PASS DP=53;AF=0.056604;SB=2;DP4=23,26,1,3 +NC_045512.2 5184 . C T 314 PASS DP=42;AF=0.261905;SB=3;DP4=12,19,6,5 +NC_045512.2 5386 . T G 210 PASS DP=55;AF=0.145455;SB=5;DP4=28,15,4,5 +NC_045512.2 5584 . A G 415 PASS DP=30;AF=0.466667;SB=0;DP4=4,11,4,11 +NC_045512.2 6402 . C T 897 PASS DP=49;AF=0.591837;SB=1;DP4=10,6,18,15 +NC_045512.2 6512 . AGTT A 115 PASS DP=29;AF=0.137931;SB=0;DP4=14,11,2,2;INDEL;HRUN=1 +NC_045512.2 7124 . C T 79 PASS DP=27;AF=0.111111;SB=0;DP4=14,9,3,1 +NC_045512.2 7851 . C T 392 PASS DP=22;AF=0.545455;SB=0;DP4=5,4,7,6 +NC_045512.2 8393 . G A 76 PASS DP=27;AF=0.111111;SB=0;DP4=16,8,2,1 +NC_045512.2 8604 . T C 80 PASS DP=20;AF=0.150000;SB=0;DP4=4,13,1,2 +NC_045512.2 8808 . A G 215 PASS DP=46;AF=0.173913;SB=0;DP4=15,20,4,7 +NC_045512.2 8986 . C T 384 PASS DP=25;AF=0.480000;SB=0;DP4=7,4,10,4 +NC_045512.2 9053 . G T 699 PASS DP=42;AF=0.523810;SB=0;DP4=12,8,13,9 +NC_045512.2 9246 . C T 66 PASS DP=60;AF=0.050000;SB=2;DP4=26,31,2,1 +NC_045512.2 9891 . C T 371 PASS DP=79;AF=0.177215;SB=1;DP4=41,23,9,6 +NC_045512.2 10029 . C T 2766 PASS DP=109;AF=0.761468;SB=0;DP4=7,13,35,54 +NC_045512.2 11201 . A G 1010 PASS DP=73;AF=0.479452;SB=0;DP4=17,20,18,18 +NC_045512.2 11282 . AGTTTGTCTG A 149 PASS DP=59;AF=0.084746;SB=7;DP4=19,35,0,5;INDEL;HRUN=1 +NC_045512.2 11332 . A G 554 PASS DP=41;AF=0.463415;SB=4;DP4=7,14,10,10 +NC_045512.2 11418 . T C 454 PASS DP=38;AF=0.394737;SB=0;DP4=13,10,8,7 +NC_045512.2 11514 . C T 523 PASS DP=42;AF=0.404762;SB=1;DP4=9,13,10,10 +NC_045512.2 12513 . C T 310 PASS DP=47;AF=0.234043;SB=0;DP4=15,21,5,6 +NC_045512.2 13019 . C T 210 PASS DP=55;AF=0.145455;SB=1;DP4=22,24,5,4 +NC_045512.2 13195 . T C 157 PASS DP=108;AF=0.064815;SB=3;DP4=68,32,4,4 +NC_045512.2 14208 . T C 115 PASS DP=73;AF=0.068493;SB=1;DP4=36,32,2,3 +NC_045512.2 14408 . C T 1502 PASS DP=45;AF=0.911111;SB=0;DP4=0,0,22,23 +NC_045512.2 15141 . C T 137 PASS DP=85;AF=0.070588;SB=0;DP4=41,36,4,4 +NC_045512.2 15240 . C T 83 PASS DP=79;AF=0.050633;SB=0;DP4=40,35,2,2 +NC_045512.2 15451 . G A 3915 PASS DP=132;AF=0.856061;SB=1;DP4=3,2,54,73 +NC_045512.2 16466 . C T 1808 PASS DP=65;AF=0.800000;SB=1;DP4=6,3,31,25 +NC_045512.2 17040 . T C 235 PASS DP=81;AF=0.123457;SB=2;DP4=32,39,6,4 +NC_045512.2 18086 . C T 479 PASS DP=59;AF=0.288136;SB=4;DP4=27,14,9,8 +NC_045512.2 18163 . A G 224 PASS DP=53;AF=0.169811;SB=1;DP4=20,24,3,6 +NC_045512.2 19220 . C T 490 PASS DP=24;AF=0.625000;SB=0;DP4=4,4,7,9 +NC_045512.2 20320 . C T 90 PASS DP=68;AF=0.058824;SB=1;DP4=30,33,3,2 +NC_045512.2 20369 . T C 68 PASS DP=60;AF=0.050000;SB=0;DP4=23,33,2,2 +NC_045512.2 21618 . C G 3270 PASS DP=105;AF=0.876190;SB=2;DP4=1,3,51,50 +NC_045512.2 21742 . C T 155 PASS DP=83;AF=0.084337;SB=0;DP4=37,38,4,4 +NC_045512.2 21846 . C T 931 PASS DP=57;AF=0.526316;SB=7;DP4=5,19,13,20 +NC_045512.2 21986 . GGTGTTTATT G 84 PASS DP=57;AF=0.052632;SB=0;DP4=35,19,2,1;INDEL;HRUN=3 +NC_045512.2 21987 . G A 1774 PASS DP=57;AF=0.842105;SB=0;DP4=0,0,35,19 +NC_045512.2 22028 . GAGTTCA G 1564 PASS DP=61;AF=0.786885;SB=0;DP4=8,7,26,22;INDEL;HRUN=1 +NC_045512.2 22193 . AATT A 159 PASS DP=89;AF=0.078652;SB=0;DP4=39,44,3,4;INDEL;HRUN=2 +NC_045512.2 22204 . T TGAGCCAGAA 194 PASS DP=82;AF=0.085366;SB=0;DP4=33,43,3,4;INDEL;HRUN=1 +NC_045512.2 22227 . C T 314 PASS DP=76;AF=0.157895;SB=2;DP4=25,35,8,8 +NC_045512.2 22578 . G A 491 PASS DP=82;AF=0.219512;SB=0;DP4=31,30,12,9 +NC_045512.2 22673 . T C 222 PASS DP=77;AF=0.116883;SB=5;DP4=29,38,2,8 +NC_045512.2 22674 . C T 225 PASS DP=77;AF=0.116883;SB=5;DP4=29,38,2,8 +NC_045512.2 22679 . T C 247 PASS DP=85;AF=0.117647;SB=10;DP4=39,36,2,8 +NC_045512.2 22686 . C T 219 PASS DP=85;AF=0.105882;SB=10;DP4=38,37,2,8 +NC_045512.2 22792 . C T 371 PASS DP=121;AF=0.123967;SB=7;DP4=66,39,13,3 +NC_045512.2 22813 . G T 122 PASS DP=152;AF=0.039474;SB=1;DP4=88,58,3,3 +NC_045512.2 22882 . T G 136 PASS DP=219;AF=0.031963;SB=1;DP4=112,98,4,5 +NC_045512.2 22898 . G A 157 PASS DP=231;AF=0.034632;SB=1;DP4=110,111,4,6 +NC_045512.2 22917 . T G 6694 PASS DP=222;AF=0.860360;SB=0;DP4=6,6,97,113 +NC_045512.2 22992 . G A 187 PASS DP=190;AF=0.047368;SB=1;DP4=84,97,5,4 +NC_045512.2 22995 . C A 6354 PASS DP=189;AF=0.936508;SB=0;DP4=0,0,88,101 +NC_045512.2 23013 . A C 192 PASS DP=168;AF=0.053571;SB=1;DP4=76,83,5,4 +NC_045512.2 23040 . A G 206 PASS DP=123;AF=0.073171;SB=0;DP4=61,50,7,5 +NC_045512.2 23048 . G A 257 PASS DP=129;AF=0.085271;SB=0;DP4=65,52,7,5 +NC_045512.2 23055 . A G 202 PASS DP=135;AF=0.066667;SB=0;DP4=68,55,6,4 +NC_045512.2 23063 . A T 282 PASS DP=138;AF=0.086957;SB=0;DP4=71,55,7,5 +NC_045512.2 23075 . T C 280 PASS DP=143;AF=0.083916;SB=0;DP4=75,56,7,5 +NC_045512.2 23403 . A G 2226 PASS DP=69;AF=0.898551;SB=0;DP4=0,0,34,35 +NC_045512.2 23525 . C T 277 PASS DP=62;AF=0.177419;SB=1;DP4=19,30,6,7 +NC_045512.2 23599 . T G 122 PASS DP=54;AF=0.092593;SB=1;DP4=27,19,5,2 +NC_045512.2 23604 . C A 170 PASS DP=54;AF=0.129630;SB=0;DP4=0,0,5,2 +NC_045512.2 23604 . C G 1377 PASS DP=54;AF=0.740741;SB=0;DP4=0,0,28,19 +NC_045512.2 23663 . G T 311 PASS DP=85;AF=0.141176;SB=1;DP4=44,27,7,6 +NC_045512.2 23854 . C A 178 PASS DP=61;AF=0.114754;SB=0;DP4=19,34,3,5 +NC_045512.2 23996 . C T 340 PASS DP=51;AF=0.235294;SB=2;DP4=23,13,8,7 +NC_045512.2 24130 . C A 69 PASS DP=48;AF=0.062500;SB=0;DP4=18,27,1,2 +NC_045512.2 24410 . G A 3323 PASS DP=116;AF=0.818965;SB=3;DP4=2,6,48,60 +NC_045512.2 24424 . A T 130 PASS DP=110;AF=0.054545;SB=0;DP4=44,60,2,4 +NC_045512.2 24469 . T A 104 PASS DP=127;AF=0.039370;SB=1;DP4=70,51,3,3 +NC_045512.2 24503 . C T 287 PASS DP=137;AF=0.094891;SB=1;DP4=71,52,7,6 +NC_045512.2 25000 . C T 189 PASS DP=37;AF=0.189189;SB=4;DP4=12,18,1,6 +NC_045512.2 25469 . C T 634 PASS DP=30;AF=0.633333;SB=1;DP4=4,5,12,9 +NC_045512.2 25584 . C T 106 PASS DP=26;AF=0.153846;SB=2;DP4=11,11,3,1 +NC_045512.2 25855 . G T 73 PASS DP=37;AF=0.081081;SB=0;DP4=16,17,2,2 +NC_045512.2 26428 . G T 301 PASS DP=100;AF=0.120000;SB=1;DP4=47,38,9,6 +NC_045512.2 26530 . A G 106 PASS DP=106;AF=0.047170;SB=1;DP4=39,61,1,4 +NC_045512.2 26577 . C G 114 PASS DP=78;AF=0.064103;SB=1;DP4=25,48,1,4 +NC_045512.2 26709 . G A 518 PASS DP=288;AF=0.079861;SB=1;DP4=149,110,15,13 +NC_045512.2 26767 . T C 8190 PASS DP=288;AF=0.819444;SB=0;DP4=13,14,128,132 +NC_045512.2 27638 . T C 1497 PASS DP=58;AF=0.758621;SB=1;DP4=4,5,25,23 +NC_045512.2 27752 . C T 1605 PASS DP=52;AF=0.865385;SB=0;DP4=2,2,21,27 +NC_045512.2 27807 . C T 134 PASS DP=59;AF=0.101695;SB=1;DP4=27,26,2,4 +NC_045512.2 27874 . C T 917 PASS DP=45;AF=0.622222;SB=2;DP4=8,9,16,12 +NC_045512.2 27900 . T C 186 PASS DP=45;AF=0.155556;SB=0;DP4=16,20,4,4 +NC_045512.2 28247 . AGATTTC A 2243 PASS DP=75;AF=0.946667;SB=5;DP4=2,5,38,33;INDEL;HRUN=1 +NC_045512.2 28270 . TA T 2891 PASS DP=87;AF=0.908046;SB=8;DP4=2,6,44,35;INDEL;HRUN=4 +NC_045512.2 28299 . A T 112 PASS DP=82;AF=0.060976;SB=0;DP4=38,38,3,3 +NC_045512.2 28461 . A G 1373 PASS DP=54;AF=0.740741;SB=3;DP4=5,4,18,27 +NC_045512.2 28881 . G T 799 PASS DP=24;AF=0.916667;SB=0;DP4=0,0,9,14 +NC_045512.2 28916 . G T 882 PASS DP=29;AF=0.862069;SB=0;DP4=2,1,15,11 +NC_045512.2 29402 . G T 1359 PASS DP=51;AF=0.764706;SB=12;DP4=1,7,22,21 +NC_045512.2 29422 . G T 72 PASS DP=41;AF=0.073171;SB=0;DP4=16,22,1,2 +NC_045512.2 29449 . G T 74 PASS DP=31;AF=0.096774;SB=0;DP4=11,17,1,2 +NC_045512.2 29742 . G T 258 PASS DP=8;AF=0.875000;SB=0;DP4=0,0,5,3 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/csv_meta.csv b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/csv_meta.csv new file mode 100644 index 0000000000..0c239ac1aa --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/csv_meta.csv @@ -0,0 +1,3 @@ +Sample,sample_collection_datetime +sample1.fastq,03/01/21 +sample13.fastq,04/03/21 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/primers.bed b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/primers.bed new file mode 100644 index 0000000000..104f878610 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-artic-variant-analysis/test-data/primers.bed @@ -0,0 +1,198 @@ +MN908947.3 25 50 SARS-CoV-2_1_LEFT pool_1 + +MN908947.3 408 431 SARS-CoV-2_1_RIGHT pool_1 - 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