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. |
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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. |
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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. |
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PE Reads Pool1 | PE Reads Pool1 | A collection of the sequencing data obtained from the **pool1** run of all samples |
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PE Reads Pool2 | PE Reads Pool2 | A collection of the sequencing data obtained from the **pool2** run of all samples |
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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) |
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Reference FASTA | Reference FASTA | The viral reference sequence to map sequenced reads against |
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Steps
ID | Name | Description |
---|---|---|
7 | Compute sequence length | toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.3 |
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/0.23.4+galaxy0 |
12 | Cut | Cut1 |
13 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
14 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+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/0.23.4+galaxy0 |
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/0.7.18 |
29 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18 |
30 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2 |
31 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 |
32 | Samtools view | toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2 |
33 | Samtools stats | toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5 |
34 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
35 | Zip collections | __ZIP_COLLECTION__ |
36 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
37 | Apply rules | __APPLY_RULES__ |
38 | Samtools merge | toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.15.1+galaxy2 |
39 | QualiMap BamQC | toolshed.g2.bx.psu.edu/repos/iuc/qualimap_bamqc/qualimap_bamqc/2.2.2d+galaxy3 |
40 | ivar trim | toolshed.g2.bx.psu.edu/repos/iuc/ivar_trim/ivar_trim/1.4.2+galaxy0 |
41 | Filter failed datasets | __FILTER_FAILED_DATASETS__ |
42 | ivar consensus | toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.4.2+galaxy0 |
43 | Flatten collection | __FLATTEN__ |
44 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
45 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
46 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
pool1_primers | pool1_primers | n/a |
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pool2_primers | pool2_primers | n/a |
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fastp_pool1_html | fastp_pool1_html | n/a |
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fastp_pool1_reads | fastp_pool1_reads | n/a |
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fastp_pool1_json | fastp_pool1_json | n/a |
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input dataset(s) (sorted) | input dataset(s) (sorted) | n/a |
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fastp_pool2_json | fastp_pool2_json | n/a |
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fastp_pool2_reads | fastp_pool2_reads | n/a |
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fastp_pool2_html | fastp_pool2_html | n/a |
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masked_ref_pool1 | masked_ref_pool1 | n/a |
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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 |
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qualimap_merged_html | qualimap_merged_html | n/a |
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trimmed_merged_mapping | trimmed_merged_mapping | n/a |
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ivar_consensus_out | ivar_consensus_out | n/a |
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per_sample_consensus | per_sample_consensus | n/a |
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quality_by_sample_report | quality_by_sample_report | n/a |
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multiqc_sample_stats | multiqc_sample_stats | n/a |
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combined_consensus_multifasta | combined_consensus_multifasta | n/a |
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Version History
v0.1 (earliest) Created 24th Feb 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
c535270
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Views: 2542 Downloads: 205 Runs: 0
Created: 24th Feb 2023 at 03:01
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