pox-virus-amplicon/main
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Workflow Type: Galaxy
Frozen
A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Allele frequency to call SNV | Allele frequency to call SNV | A consensus **SNV** call requires that the alternate base is seen in at least this fraction of reads covering it. |
|
| Allele frequency to call indel | Allele frequency to call indel | A consensus **indel** call requires that the indel is seen in at least this fraction of reads covering it. |
|
| Minimum quality score to call base | Minimum quality score to call base | Only sequenced bases with at least this base calling quality will be considered for consensus calling. |
|
| PE Reads Pool1 | PE Reads Pool1 | A collection of the sequencing data obtained from the **pool1** run of all samples |
|
| PE Reads Pool2 | PE Reads Pool2 | A collection of the sequencing data obtained from the **pool2** run of all samples |
|
| Primer Scheme | Primer Scheme | The workflow expects a primer scheme split into two separate sequencing pools. These pools must be denoted as pool1/pool2 in the BED score column. The pool ids may, optionally, be followed by indicators of the subpool for tiled PCR amplification (e.g., pool1a/pool1b/pool2a/pool2b) |
|
| Reference FASTA | Reference FASTA | The viral reference sequence to map sequenced reads against |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Compute sequence length | toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4 |
| 8 | Select pool1 primers | Grep1 |
| 9 | Select pool2 primers | Grep1 |
| 10 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
| 11 | fastp: Trimmed Illumina Reads Pool1 | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy2 |
| 12 | Cut | Cut1 |
| 13 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0 |
| 14 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.9+galaxy0 |
| 15 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 |
| 16 | Sort collection | __SORTLIST__ |
| 17 | Get end position of sequence | param_value_from_file |
| 18 | Get end position of Pool1 | param_value_from_file |
| 19 | Get start position of Pool2 | param_value_from_file |
| 20 | Parse parameter value | param_value_from_file |
| 21 | fastp: Trimmed Illumina Reads Pool2 | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.1+galaxy2 |
| 22 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 23 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 24 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 25 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 26 | Mask Reference for Pool1 | toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0 |
| 27 | Mask Reference for Pool2 | toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: maskseq51/5.0.0 |
| 28 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19 |
| 29 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19 |
| 30 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0 |
| 31 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7 |
| 32 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0 |
| 33 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.7 |
| 34 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 35 | Zip collections | __ZIP_COLLECTION__ |
| 36 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 37 | Apply rules | __APPLY_RULES__ |
| 38 | Samtools merge | toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0 |
| 39 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.3+galaxy0 |
| 40 | ivar trim | toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.4+galaxy1 |
| 41 | Filter failed datasets | __FILTER_FAILED_DATASETS__ |
| 42 | ivar consensus | toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.4+galaxy0 |
| 43 | Flatten collection | __FLATTEN__ |
| 44 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.5+galaxy2 |
| 45 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 |
| 46 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| pool1_primers | pool1_primers | n/a |
|
| pool2_primers | pool2_primers | n/a |
|
| fastp_pool1_html | fastp_pool1_html | n/a |
|
| fastp_pool1_reads | fastp_pool1_reads | n/a |
|
| fastp_pool1_json | fastp_pool1_json | n/a |
|
| input dataset(s) (sorted) | input dataset(s) (sorted) | n/a |
|
| fastp_pool2_json | fastp_pool2_json | n/a |
|
| fastp_pool2_reads | fastp_pool2_reads | n/a |
|
| fastp_pool2_html | fastp_pool2_html | n/a |
|
| masked_ref_pool1 | masked_ref_pool1 | n/a |
|
| masked_ref_pool2 | masked_ref_pool2 | n/a |
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| Mapping of Pool1 | Mapping of Pool1 | n/a |
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| mapping_pool2 | mapping_pool2 | n/a |
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| filtered_mapping_pool1 | filtered_mapping_pool1 | n/a |
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| mapping_stats_pool1 | mapping_stats_pool1 | n/a |
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| filtered_mapping_pool2 | filtered_mapping_pool2 | n/a |
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| mapping_stats_pool2 | mapping_stats_pool2 | n/a |
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| multiqc_pool1_stats | multiqc_pool1_stats | n/a |
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| pool1_quality_report | pool1_quality_report | n/a |
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| pool2_quality_report | pool2_quality_report | n/a |
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| multiqc_pool2_stats | multiqc_pool2_stats | n/a |
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| mapping_merged | mapping_merged | n/a |
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| qualimap_pool1_raw | qualimap_pool1_raw | n/a |
|
| qualimap_merged_html | qualimap_merged_html | n/a |
|
| trimmed_merged_mapping | trimmed_merged_mapping | n/a |
|
| ivar_consensus_out | ivar_consensus_out | n/a |
|
| per_sample_consensus | per_sample_consensus | n/a |
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| quality_by_sample_report | quality_by_sample_report | n/a |
|
| multiqc_sample_stats | multiqc_sample_stats | n/a |
|
| combined_consensus_multifasta | combined_consensus_multifasta | n/a |
|
Version History
v0.1 (earliest) Created 24th Feb 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1c535270
Creators and Submitter
License
Activity
Views: 6578 Downloads: 2391 Runs: 3
Created: 24th Feb 2023 at 03:01
Last updated: 18th Aug 2025 at 18:43
AttributionsNone
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