pox-virus-amplicon/main

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Workflow Type: Galaxy

A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach

SEEK ID: https://workflowhub.eu/workflows/439?version=2

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.
  • float?
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.
  • float?
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.
  • int?
PE Reads Pool1 PE Reads Pool1 A collection of the sequencing data obtained from the **pool1** run of all samples
  • File[]
PE Reads Pool2 PE Reads Pool2 A collection of the sequencing data obtained from the **pool2** run of all samples
  • File[]
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)
  • File
Reference FASTA Reference FASTA The viral reference sequence to map sequenced reads against
  • File

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
  • File
pool2_primers pool2_primers n/a
  • File
fastp_pool1_html fastp_pool1_html n/a
  • File
fastp_pool1_reads fastp_pool1_reads n/a
  • File
fastp_pool1_json fastp_pool1_json n/a
  • File
input dataset(s) (sorted) input dataset(s) (sorted) n/a
  • File
fastp_pool2_json fastp_pool2_json n/a
  • File
fastp_pool2_reads fastp_pool2_reads n/a
  • File
fastp_pool2_html fastp_pool2_html n/a
  • File
masked_ref_pool1 masked_ref_pool1 n/a
  • File
masked_ref_pool2 masked_ref_pool2 n/a
  • File
Mapping of Pool1 Mapping of Pool1 n/a
  • File
mapping_pool2 mapping_pool2 n/a
  • File
filtered_mapping_pool1 filtered_mapping_pool1 n/a
  • File
mapping_stats_pool1 mapping_stats_pool1 n/a
  • File
filtered_mapping_pool2 filtered_mapping_pool2 n/a
  • File
mapping_stats_pool2 mapping_stats_pool2 n/a
  • File
multiqc_pool1_stats multiqc_pool1_stats n/a
  • File
pool1_quality_report pool1_quality_report n/a
  • File
pool2_quality_report pool2_quality_report n/a
  • File
multiqc_pool2_stats multiqc_pool2_stats n/a
  • File
mapping_merged mapping_merged n/a
  • File
qualimap_pool1_raw qualimap_pool1_raw n/a
  • File
qualimap_merged_html qualimap_merged_html n/a
  • File
trimmed_merged_mapping trimmed_merged_mapping n/a
  • File
ivar_consensus_out ivar_consensus_out n/a
  • File
per_sample_consensus per_sample_consensus n/a
  • File
quality_by_sample_report quality_by_sample_report n/a
  • File
multiqc_sample_stats multiqc_sample_stats n/a
  • File
combined_consensus_multifasta combined_consensus_multifasta n/a
  • File

Version History

v0.2 (latest) Created 22nd Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 fbc1f35

v0.1 (earliest) Created 24th Feb 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 c535270
help Creators and Submitter
Creators
  • Viktoria Isabel Schwarz
  • Wolfgang Maier
Submitter
License
MIT License
Activity

Views: 3076   Downloads: 276   Runs: 0

Created: 24th Feb 2023 at 03:01

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