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Merge pull request #584 from Smeds/update-pretext
feat: updated version of pretext workflow developed by Delphine that takes HiFi and HiC as input.
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‎workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/.dockstore.yml‎

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version: 1.2
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workflows:
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- name: main
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subclass: Galaxy
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publish: true
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primaryDescriptorPath: /hi-c-map-for-assembly-manual-curation.ga
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testParameterFiles:
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- /hi-c-map-for-assembly-manual-curation-tests.yml
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authors:
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- name: Patrik Smeds
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orcid: 0000-0001-6228-2785
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- name: Delphine Lariviere
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orcid: 0000-0001-6421-3484

‎workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/CHANGELOG.md‎

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# Changelog
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## [1.0beta1] 2024-11-12
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- Creation of a workflow for the generation of Hi-C Maps with coverage, gaps and Telomere Tracks

‎workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/README.md‎

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# Hi-C Contact map generation for manual curation of genome assemblies
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This workflow generates Hi-C contact maps for diploid genome assemblies in the Pretext format. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.
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## Inputs
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1. **Haplotype 1** [fasta]
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2. **Will you use a second haplotype?**
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3. **Haplotype 2** [fasta]
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4. **Do you want to add suffixes to the scaffold names?** Select yes if the scaffold names in your assembly do not contain haplotype information.
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5. **Haplotype 1 suffix** This suffix will be added to haplotype 1 scaffold names if you selected to add suffixes to the scaffold names.
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6. **Haplotype 2 suffix** This suffix will be added to haplotype 2 scaffold names if you selected to add suffixes to the scaffold names.
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7. **Hi-C reads** [fastq] Paired Collection containing the Hi-D data
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8. **Do you want to trim the Hi-C data?** If *yes*, remove 5bp at the end of Hi-C reads. Use with Arima Hi-C data if the Hi-C map looks "noisy".
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9. **Telomere repeat to suit species** Expected value of the repeated sequences in the telomeres. Default value [CCCTAA] is suited to vertebrates.
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10. **PacBio reads** [fastq] Collection of PacBio reads.
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## Outputs
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1. Concatenated Assembly [fasta] If two haplotypes are used.
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2. Trimmed Hi-C data (If trimming option is selected) [fastq]
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3. Mapped Hi-C reads [bam]
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4. Telomeres track [bedgraph]
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5. Gap track [bedgraph]
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6. Coverage track [bigwig]
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7. Pretext Map without tracks [pretext]
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8. Pretext Map with tracks [pretext]
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9. Pretext Snapshot image of the Hi-C contact map [png]

‎workflows/VGP-assembly-v2/hi-c-contact-map-for-assembly-manual-curation/hi-c-map-for-assembly-manual-curation-tests.yml‎

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- doc: Test outline for hi-c-map-for-assembly-manual-curation.ga 1
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job:
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Haplotype 1:
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class: File
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location: https://zenodo.org/records/14230702/files/Haplotype%202.fasta
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filetype: fasta
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Haplotype 2:
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class: File
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location: https://zenodo.org/records/14230702/files/Haplotype%202.fasta
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filetype: fasta
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Hi-C reads:
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class: Collection
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collection_type: list:paired
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elements:
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- class: Collection
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type: paired
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identifier: Hi-C reads
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elements:
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- identifier: forward
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class: File
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path: https://zenodo.org/records/14230702/files/HiC%20forward.fastqsanger.gz
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- identifier: reverse
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class: File
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path: https://zenodo.org/records/14230702/files/HiC%20reverse.fastqsanger.gz
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PacBio reads:
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class: Collection
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collection_type: list
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elements:
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- class: File
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identifier: PacBio reads.fastq.gz
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location: https://zenodo.org/records/14230702/files/PacBio%20reads.fastq.gz
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Do you want to add suffixes to the scaffold names?: true
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Will you use a second haplotype?: false
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First Haplotype suffix: H1
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Second Haplotype suffix: H2
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Do you want to trim the Hi-C data?: true
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Telomere repeat to suit species: CCCTAA
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outputs:
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Assembly for curation:
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asserts:
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has_text:
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text: ">scaffold_10.H1"
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Gaps Bed:
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asserts:
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has_text:
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text: "scaffold_10.H1 835498 835698"
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Seqtk-telo Output:
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asserts:
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has_text:
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text: "scaffold_10.H1 0 11012 139653677"
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Gaps Bedgraph:
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asserts:
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has_text:
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text: "scaffold_10.H1 835498 835698 200"
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BigWig Coverage:
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asserts:
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has_size:
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value : 100000
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delta: 40000
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Telomeres Bedgraph:
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asserts:
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has_text:
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text: "scaffold_10.H1 0 11012 11012"
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Merged Hi-C Alignments:
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asserts:
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has_size:
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value : 400000000
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delta: 50000000
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Pretext All tracks:
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asserts:
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has_size:
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value : 1700000
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delta: 500000
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- doc: Test outline for hi-c-map-for-assembly-manual-curation.ga 2
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job:
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Haplotype 1:
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class: File
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location: https://zenodo.org/records/14230702/files/Haplotype%201.fasta
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filetype: fasta
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Haplotype 2:
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class: File
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location: https://zenodo.org/records/14230702/files/Haplotype%201.fasta
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filetype: fasta
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Hi-C reads:
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class: Collection
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collection_type: list:paired
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elements:
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- class: Collection
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type: paired
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identifier: Hi-C reads
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elements:
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- identifier: forward
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class: File
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path: https://zenodo.org/records/14230702/files/HiC%20forward.fastqsanger.gz
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- identifier: reverse
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class: File
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path: https://zenodo.org/records/14230702/files/HiC%20reverse.fastqsanger.gz
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PacBio reads:
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class: Collection
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collection_type: list
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elements:
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- class: File
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identifier: PacBio reads.fastq.gz
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location: https://zenodo.org/records/14230702/files/PacBio%20reads.fastq.gz
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Do you want to add suffixes to the scaffold names?: true
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Will you use a second haplotype?: false
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First Haplotype suffix: H1
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Second Haplotype suffix: H2
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Do you want to trim the Hi-C data?: true
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Telomere repeat to suit species: CCCTAA
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outputs:
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Assembly for curation:
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asserts:
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has_text:
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text: ">scaffold_10.H1"
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Gaps Bed:
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asserts:
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has_text:
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text: "scaffold_10.H1 34145604 34145804"
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Gaps Bedgraph:
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asserts:
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has_text:
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text: "scaffold_10.H1 34145604 34145804 200"
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BigWig Coverage:
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asserts:
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has_size:
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value : 100000
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delta: 40000
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Merged Hi-C Alignments:
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asserts:
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has_size:
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value : 400000000
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delta: 50000000
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Pretext All tracks:
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asserts:
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has_size:
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value : 1600000
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delta: 500000
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