diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/.dockstore.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/.dockstore.yml new file mode 100644 index 0000000000..69e1e2f211 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-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-metatranscriptomic-PE-data-with-Freyja.ga + testParameterFiles: + - /SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja-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-metatranscriptomic-variant-analysis/CHANGELOG.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/CHANGELOG.md new file mode 100644 index 0000000000..bad42c986a --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/CHANGELOG.md @@ -0,0 +1,5 @@ +# Changelog + +## [0.1] + +- Initial version of COVID-19: variation analysis on wastewater metatranscriptomic PE data workflow diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/README.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/README.md new file mode 100644 index 0000000000..d01a5d6b32 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/README.md @@ -0,0 +1,4 @@ +SARS-CoV-2 wastewater surveillance: lineages analysis on metatranscriptomic PE data +--------------------------------------------- + +The workflow for SARS-CoV-2 wastewater Illumina-sequenced metatranscriptomic data analysis diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja-tests.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja-tests.yml new file mode 100644 index 0000000000..2d3de403fc --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja-tests.yml @@ -0,0 +1,37 @@ +- doc: Test outline for SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja + job: + VCF: + class: Collection + collection_type: list + elements: + - class: File + identifier: SRR12596170.fastq + path: test-data/VCF_SRR12596170.fastq.vcf + - class: File + identifier: SRR12596172.fastq + path: test-data/VCF_SRR12596172.fastq.vcf + BAM collection of aligned and preprocessed reads: + class: Collection + collection_type: list + elements: + - class: File + identifier: SRR12596170.fastq + path: test-data/BAM collection of aligned and preprocessed reads_SRR12596170.fastq.bam + - class: File + identifier: SRR12596172.fastq + path: test-data/BAM collection of aligned and preprocessed reads_SRR12596172.fastq.bam + Time(s) metadata CSV file: + class: File + identifier: csv_meta.csv + path: test-data/csv_meta.csv + outputs: + 'Freyja: Demix on input dataset(s): Lineages abundances summary': + element_tests: + SRR12596170.fastq: + asserts: + has_text: + text: "Other" + SRR12596172.fastq: + asserts: + has_text: + text: "coverage" \ No newline at end of file diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja.ga b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja.ga new file mode 100644 index 0000000000..39188dad7b --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/SARS-CoV-2-wastewater-analysis-from-metatranscriptomic-PE-data-with-Freyja.ga @@ -0,0 +1,365 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "A workflow for SARS-CoV-2 lineage analysis from metatranscriptomic paired-end sequencing data of wastewater samples", + "creator": [ + { + "class": "Person", + "identifier": "0000-0002-0507-4602", + "name": "Polina Polunina" + }, + { + "class": "Person", + "identifier": "0000-0001-9852-1987", + "name": "B\u00e9r\u00e9nice Batut" + }, + { + "class": "Person", + "identifier": "0000-0002-9464-6640", + "name": "Wolfgang Maier" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "SARS-CoV-2 wastewater analysis from metatranscriptome PE data with Freyja and Cojac", + "steps": { + "0": { + "annotation": "VCF file containing SARS-CoV-2 variant calls", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "VCF file containing SARS-CoV-2 variant calls", + "name": "VCF" + } + ], + "label": "VCF", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 0.52734375, + "top": 21.0546875 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"vcf\"], \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "be2ab7bf-00c2-401f-84c5-6e03b3457104", + "when": null, + "workflow_outputs": [] + }, + "1": { + "annotation": "Fully processed reads for variant calling (primer-trimmed, realigned reads with added indelquals)", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Fully processed reads for variant calling (primer-trimmed, realigned reads with added indelquals)", + "name": "BAM collection of aligned and preprocessed reads" + } + ], + "label": "BAM collection of aligned and preprocessed reads", + "name": "Input dataset collection", + "outputs": [], + "position": { + "left": 0, + "top": 146.55791931039266 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"bam\"], \"tag\": null, \"collection_type\": \"list\"}", + "tool_version": null, + "type": "data_collection_input", + "uuid": "f023cdf9-8880-451e-9f5b-cf77b865ee27", + "when": null, + "workflow_outputs": [] + }, + "2": { + "annotation": "A time(s) metadata CSV file should have Sample,sample_collection_datetime form or Sample,sample_collection_datetime,viral_load form", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "A time(s) metadata CSV file should have Sample,sample_collection_datetime form or Sample,sample_collection_datetime,viral_load form", + "name": "Time(s) metadata CSV file" + } + ], + "label": "Time(s) metadata CSV file", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 1299.02745527328, + "top": 397.122185080986 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"csv\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "294b0754-dc6e-4341-9125-d436a5221a37", + "when": null, + "workflow_outputs": [] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy0", + "errors": null, + "id": 3, + "input_connections": { + "input_bams": { + "id": 1, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Samtools depth", + "outputs": [ + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 401.38671875, + "top": 167.96875 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.15.1+galaxy0", + "tool_shed_repository": { + "changeset_revision": "56faa6a57e50", + "name": "samtools_depth", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"additional_options\": {\"required_flags\": null, \"skipped_flags\": [\"4\", \"256\", \"512\", \"1024\"], \"deletions\": false, \"single_read\": false}, \"all\": \"\", \"basequality\": null, \"cond_region\": {\"select_region\": \"no\", \"__current_case__\": 0}, \"input_bams\": {\"__class__\": \"ConnectedValue\"}, \"mapquality\": null, \"maxdepth\": null, \"minlength\": null, \"output_options\": {\"header\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.15.1+galaxy0", + "type": "tool", + "uuid": "ebda63f3-e291-44a9-a79b-9c5aa212d4ee", + "when": null, + "workflow_outputs": [ + { + "label": "Samtools depth on input dataset(s)", + "output_name": "output", + "uuid": "dce385dc-1289-42fb-acf2-80ca443b2f40" + } + ] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_demix/freyja_demix/1.4.4+galaxy0", + "errors": null, + "id": 4, + "input_connections": { + "depth_file": { + "id": 3, + "output_name": "output" + }, + "variants_in": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Freyja: Demix", + "name": "meta" + } + ], + "label": null, + "name": "Freyja: Demix", + "outputs": [ + { + "name": "abundances", + "type": "tabular" + } + ], + "position": { + "left": 700.546875, + "top": 0 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_demix/freyja_demix/1.4.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "c0a0e79d7196", + "name": "freyja_demix", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"confirmedonly\": false, \"depth_cutoff\": \"10\", \"depth_file\": {\"__class__\": \"ConnectedValue\"}, \"eps\": null, \"meta\": {\"__class__\": \"RuntimeValue\"}, \"sample_name\": {\"source\": \"auto\", \"__current_case__\": 0}, \"usher_update_option\": {\"choice\": \"repo\", \"__current_case__\": 0}, \"variants_in\": {\"__class__\": \"ConnectedValue\"}, \"wgisaid\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.4.4+galaxy0", + "type": "tool", + "uuid": "ec1ae9de-77bf-4475-afea-c390dac18ef6", + "when": null, + "workflow_outputs": [ + { + "label": "Freyja: Demix on input dataset(s): Lineages abundances summary", + "output_name": "abundances", + "uuid": "b2b4a13d-422f-4557-b21e-028fca787301" + } + ] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.4.4+galaxy0", + "errors": null, + "id": 5, + "input_connections": { + "need_aggregation|demix_file": { + "id": 4, + "output_name": "abundances" + } + }, + "inputs": [], + "label": null, + "name": "Freyja: Aggregate and visualize", + "outputs": [ + { + "name": "aggregated", + "type": "tabular" + }, + { + "name": "abundances_plot", + "type": "pdf" + } + ], + "position": { + "left": 997.3323006587863, + "top": 194.51176309945092 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.4.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "1f89eeba299a", + "name": "freyja_aggregate_plot", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"need_aggregation\": {\"choice\": \"yes\", \"__current_case__\": 0, \"demix_file\": {\"__class__\": \"ConnectedValue\"}}, \"plot_format\": {\"choice\": \"plot\", \"__current_case__\": 0, \"need_metadata\": {\"choice\": \"no\", \"__current_case__\": 1}, \"lineages\": false, \"mincov\": \"0.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.4.4+galaxy0", + "type": "tool", + "uuid": "a9502780-4d28-4440-9acb-837a35aa1758", + "when": null, + "workflow_outputs": [ + { + "label": "Freyja: Aggregate and visualize on input dataset(s): Lineages abundances plot", + "output_name": "abundances_plot", + "uuid": "3e15daec-03c4-42b9-b58f-24dc8ac72616" + }, + { + "label": "Freyja: Aggregate and visualize on input dataset(s): Aggregated data", + "output_name": "aggregated", + "uuid": "82d7322d-f594-4292-82d9-8bb64949836a" + } + ] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.4.4+galaxy0", + "errors": null, + "id": 6, + "input_connections": { + "need_aggregation|tsv_aggregated": { + "id": 5, + "output_name": "aggregated" + }, + "plot_format|need_metadata|csv_meta": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": "Freyja plot over time (month bins)", + "name": "Freyja: Aggregate and visualize", + "outputs": [ + { + "name": "abundances_plot", + "type": "pdf" + } + ], + "position": { + "left": 1603.4306620133507, + "top": 6.067128895183275 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.4.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "1f89eeba299a", + "name": "freyja_aggregate_plot", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"need_aggregation\": {\"choice\": \"no\", \"__current_case__\": 1, \"tsv_aggregated\": {\"__class__\": \"ConnectedValue\"}}, \"plot_format\": {\"choice\": \"plot\", \"__current_case__\": 0, \"need_metadata\": {\"choice\": \"yes\", \"__current_case__\": 0, \"csv_meta\": {\"__class__\": \"ConnectedValue\"}, \"interval\": \"MS\"}, \"lineages\": false, \"mincov\": \"0.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.4.4+galaxy0", + "type": "tool", + "uuid": "89e7f355-72ed-40d5-81fc-6d5e42328446", + "when": null, + "workflow_outputs": [ + { + "label": "Freyja: Lineages abundances plot over time (month bins)", + "output_name": "abundances_plot", + "uuid": "cac15b18-74f9-491e-9bad-74b8e2fa9c74" + } + ] + }, + "7": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.4.4+galaxy0", + "errors": null, + "id": 7, + "input_connections": { + "need_aggregation|tsv_aggregated": { + "id": 5, + "output_name": "aggregated" + }, + "plot_format|need_metadata|csv_meta": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [], + "label": "Freyja plot over time (day bins)", + "name": "Freyja: Aggregate and visualize", + "outputs": [ + { + "name": "abundances_plot", + "type": "pdf" + } + ], + "position": { + "left": 1603.9128849862218, + "top": 300.4812560741751 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/freyja_aggregate_plot/freyja_aggregate_plot/1.4.4+galaxy0", + "tool_shed_repository": { + "changeset_revision": "1f89eeba299a", + "name": "freyja_aggregate_plot", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"need_aggregation\": {\"choice\": \"no\", \"__current_case__\": 1, \"tsv_aggregated\": {\"__class__\": \"ConnectedValue\"}}, \"plot_format\": {\"choice\": \"plot\", \"__current_case__\": 0, \"need_metadata\": {\"choice\": \"yes\", \"__current_case__\": 0, \"csv_meta\": {\"__class__\": \"ConnectedValue\"}, \"interval\": \"D\"}, \"lineages\": false, \"mincov\": \"0.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.4.4+galaxy0", + "type": "tool", + "uuid": "0fbb4400-00a0-4a61-8da5-e7915e7a6298", + "when": null, + "workflow_outputs": [ + { + "label": "Freyja: Lineages abundances plot (day bins)", + "output_name": "abundances_plot", + "uuid": "9c565e04-74f8-4bc6-8d5c-c21e22743a63" + } + ] + } + }, + "tags": [ + "wastewater", + "v2", + "metatranscriptome" + ], + "uuid": "cfc5d065-46fb-45c5-a9cb-f86c92d5ca26", + "version": 8 +} \ No newline at end of file diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_SRR12596170.fastq.bam b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_SRR12596170.fastq.bam new file mode 100644 index 0000000000..e1cf131b6c Binary files /dev/null and b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_SRR12596170.fastq.bam differ diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_SRR12596172.fastq.bam b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_SRR12596172.fastq.bam new file mode 100644 index 0000000000..e0154be725 Binary files /dev/null and b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/BAM collection of aligned and preprocessed reads_SRR12596172.fastq.bam differ diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/VCF_SRR12596170.fastq.vcf b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/VCF_SRR12596170.fastq.vcf new file mode 100644 index 0000000000..992029579d --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/VCF_SRR12596170.fastq.vcf @@ -0,0 +1,37 @@ +##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/052/597/52597958/working/pp-tmp/lofreq2_call_parallelbccur8uj/0.vcf.gz reads.bam +##reference=reference.fa +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= 0.001000"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 241 . C T 522 PASS DP=16;AF=0.937500;SB=0;DP4=1,0,7,8 +NC_045512.2 3037 . C T 251 PASS DP=7;AF=1.000000;SB=0;DP4=0,0,5,2 +NC_045512.2 8077 . A AAG 63 PASS DP=11;AF=0.181818;SB=4;DP4=8,1,1,1;INDEL;HRUN=2 +NC_045512.2 9105 . G GT 68 PASS DP=11;AF=0.181818;SB=0;DP4=5,4,1,1;INDEL;HRUN=3 +NC_045512.2 12233 . GA G 68 PASS DP=6;AF=0.333333;SB=0;DP4=1,3,0,2;INDEL;HRUN=2 +NC_045512.2 14408 . C T 179 PASS DP=5;AF=1.000000;SB=0;DP4=0,0,4,1 +NC_045512.2 15965 . G GT 70 PASS DP=7;AF=0.285714;SB=0;DP4=3,2,2,0;INDEL;HRUN=4 +NC_045512.2 23403 . A G 414 PASS DP=14;AF=0.928571;SB=0;DP4=1,0,7,6 +NC_045512.2 24263 . C CA 68 PASS DP=11;AF=0.181818;SB=3;DP4=2,7,1,1;INDEL;HRUN=3 +NC_045512.2 24966 . A T 83 PASS DP=9;AF=0.333333;SB=2;DP4=2,4,2,1 +NC_045512.2 25563 . G T 348 PASS DP=15;AF=0.733333;SB=2;DP4=1,3,6,5 +NC_045512.2 25947 . G C 84 PASS DP=12;AF=0.250000;SB=2;DP4=3,6,2,1 +NC_045512.2 27271 . G GT 66 PASS DP=11;AF=0.181818;SB=0;DP4=4,8,0,2;INDEL;HRUN=3 +NC_045512.2 27964 . C T 199 PASS DP=20;AF=0.350000;SB=1;DP4=4,9,3,4 +NC_045512.2 28009 . T C 64 PASS DP=21;AF=0.142857;SB=0;DP4=10,8,2,1 +NC_045512.2 28214 . C CT 57 PASS DP=28;AF=0.071429;SB=0;DP4=14,12,1,1;INDEL;HRUN=5 +NC_045512.2 28881 . G A 99 PASS DP=24;AF=0.166667;SB=8;DP4=6,14,3,1 +NC_045512.2 28882 . G A 98 PASS DP=24;AF=0.166667;SB=8;DP4=6,14,3,1 +NC_045512.2 28883 . G C 115 PASS DP=25;AF=0.200000;SB=5;DP4=6,14,3,2 +NC_045512.2 29051 . C CA 181 PASS DP=21;AF=0.285714;SB=1;DP4=5,10,3,3;INDEL;HRUN=5 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/VCF_SRR12596172.fastq.vcf b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/VCF_SRR12596172.fastq.vcf new file mode 100644 index 0000000000..44f39ea2ae --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/VCF_SRR12596172.fastq.vcf @@ -0,0 +1,43 @@ +##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/jwd/main/052/597/52597959/working/pp-tmp/lofreq2_call_parallelqx9d6_oq/0.vcf.gz reads.bam +##reference=reference.fa +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##FILTER= 0.001000"> +#CHROM POS ID REF ALT QUAL FILTER INFO +NC_045512.2 241 . C T 1497 PASS DP=46;AF=0.978261;SB=0;DP4=0,0,30,16 +NC_045512.2 1059 . C T 2987 PASS DP=97;AF=0.917526;SB=4;DP4=3,1,40,53 +NC_045512.2 2040 . C T 253 PASS DP=130;AF=0.092308;SB=1;DP4=75,43,7,5 +NC_045512.2 3037 . C T 4313 PASS DP=136;AF=0.977941;SB=0;DP4=0,0,75,61 +NC_045512.2 11074 . CT C 152 PASS DP=103;AF=0.087379;SB=0;DP4=46,48,4,5;INDEL;HRUN=8 +NC_045512.2 13541 . C CT 102 PASS DP=117;AF=0.034188;SB=5;DP4=85,30,2,2;INDEL;HRUN=4 +NC_045512.2 14408 . C T 2987 PASS DP=89;AF=0.955056;SB=0;DP4=0,0,56,31 +NC_045512.2 14625 . C CT 117 PASS DP=150;AF=0.033333;SB=4;DP4=78,67,4,1;INDEL;HRUN=4 +NC_045512.2 15559 . C CT 97 PASS DP=157;AF=0.025478;SB=8;DP4=67,87,0,4;INDEL;HRUN=4 +NC_045512.2 17825 . C T 166 PASS DP=118;AF=0.067797;SB=1;DP4=40,70,2,6 +NC_045512.2 18487 . A G 167 PASS DP=111;AF=0.072072;SB=7;DP4=46,55,2,8 +NC_045512.2 20844 . C T 1460 PASS DP=107;AF=0.495327;SB=3;DP4=26,26,32,23 +NC_045512.2 21569 . G GT 70 PASS DP=170;AF=0.023529;SB=5;DP4=64,103,3,1;INDEL;HRUN=5 +NC_045512.2 22329 . C T 134 PASS DP=105;AF=0.066667;SB=3;DP4=47,50,5,2 +NC_045512.2 23403 . A G 3348 PASS DP=108;AF=0.962963;SB=0;DP4=0,0,60,48 +NC_045512.2 23554 . A G 139 PASS DP=141;AF=0.056738;SB=25;DP4=61,72,8,0 +NC_045512.2 24672 . CA C 100 PASS DP=104;AF=0.038462;SB=9;DP4=51,49,4,0;INDEL;HRUN=5 +NC_045512.2 25563 . G T 3725 PASS DP=112;AF=0.973214;SB=0;DP4=0,1,48,61 +NC_045512.2 27481 . C CT 73 PASS DP=122;AF=0.024590;SB=0;DP4=83,37,2,1;INDEL;HRUN=4 +NC_045512.2 27964 . C T 3518 PASS DP=130;AF=0.823077;SB=0;DP4=6,12,36,76 +NC_045512.2 28378 . G T 84 PASS DP=134;AF=0.037313;SB=1;DP4=55,74,3,2 +NC_045512.2 28881 . G A 91 PASS DP=123;AF=0.040650;SB=1;DP4=60,58,2,3 +NC_045512.2 28882 . G A 88 PASS DP=122;AF=0.040984;SB=1;DP4=60,56,2,3 +NC_045512.2 28883 . G C 89 PASS DP=121;AF=0.041322;SB=1;DP4=59,57,2,3 +NC_045512.2 28987 . CCAA C 109 PASS DP=99;AF=0.040404;SB=0;DP4=37,60,1,3;INDEL;HRUN=2 +NC_045512.2 29051 . C CA 190 PASS DP=98;AF=0.071429;SB=1;DP4=29,62,3,4;INDEL;HRUN=5 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/csv_meta.csv b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/csv_meta.csv new file mode 100644 index 0000000000..ee1094667e --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/test-data/csv_meta.csv @@ -0,0 +1,3 @@ +Sample,sample_collection_datetime +SRR12596172.fastq,03/01/21 +SRR12596170.fastq,04/03/21 diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/tools.yml b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/tools.yml new file mode 100644 index 0000000000..139c0a62a0 --- /dev/null +++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-wastewater-pe-illumina-metatranscriptomic-variant-analysis/tools.yml @@ -0,0 +1,23 @@ +install_tool_dependencies: True +install_repository_dependencies: True +install_resolver_dependencies: True + +tools: +- name: samtools_depth + owner: iuc + revisions: + - 56faa6a57e50 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: freyja_demix + owner: iuc + revisions: + - c0a0e79d7196 + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/ +- name: freyja_aggregate_plot + owner: iuc + revisions: + - 1f89eeba299a + tool_panel_section_label: Tools from workflows + tool_shed_url: https://toolshed.g2.bx.psu.edu/