diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md new file mode 100644 index 000000000..59cbaa2a5 --- /dev/null +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/CHANGELOG.md @@ -0,0 +1,7 @@ +# Changelog + +## [0.1] - 2024-02-07 + +### Added + +- Workflow for purging duplication in contigs in single haplotype \ No newline at end of file diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml new file mode 100644 index 000000000..ac92c93fe --- /dev/null +++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b-tests.yml @@ -0,0 +1,76 @@ +- doc: Test outline for Purging-duplicates-one-haplotype-VGP6b + job: + Genomescope model parameters: + class: File + location: https://www.dropbox.com/scl/fi/6a6b9xc6jih3rtfrfy7ch/Genomescope-model-parameters.tabular?rlkey=2d86kp0wsdlzk5bxzvs36ry4a&dl=1 + filetype: tabular + Assembly to purge: + class: File + location: https://www.dropbox.com/scl/fi/7hbeju59zkbc5d28lpp19/hap1.fasta?rlkey=xii6j4iq0y48f5qulu0nti8uu&dl=1 + filetype: fasta + Meryl Database: + class: File + location: https://www.dropbox.com/scl/fi/gpkhbn9onssi5z776kwzy/Meryl-Database.meryldb?rlkey=2ozjdiego6ew9nwaxjgmw3a79&dl=1 + filetype: meryldb + Estimated genome size - Parameter File: + class: File + location: https://www.dropbox.com/scl/fi/s1jieqs34p5ol3xjcez39/Estimated-genome-size-Parameter-File.expression.json?rlkey=bamnfmxo7mqk7y3gq59v5rrzb&dl=1 + filetype: expression.json + Assembly to leave alone (need this for merqury): + class: File + location: https://www.dropbox.com/scl/fi/xz7v21ora7n86iisopr8i/hap2.fasta?rlkey=91vdm0bes0a77kaz17rwv759y&dl=1 + filetype: fasta + Pacbio Reads Collection - Trimmed: + class: Collection + collection_type: list + elements: + - class: File + identifier: yeast_reads_sub1.fastq.gz + location: https://www.dropbox.com/scl/fi/1xmp7kajhdp5cnm4nc8qj/Trimmed_yeast_reads_sub1.fastq.gz?rlkey=q7e54x26fm6fp732kp2lz6bxf&dl=1 + Name of un-altered assembly: Hap2 + Name of purged assembly: Hap1 + outputs: + Removed haplotigs: + asserts: + has_n_lines: + n: 14 + Purged assembly: + asserts: + has_n_lines: + n: 158 + Purged assembly (GFA): + asserts: + has_n_lines: + n: 160 + Assembly statistics: + asserts: + has_text: + text: "Average contig length 23,851.86 24,476.28" + Cutoffs: + asserts: + has_text: + text: "1 15 15 16 16 48" + 'Busco on Purged Primary assembly: short summary': + asserts: + has_text: + text: "C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354" + Purged assembly statistics: + asserts: + has_text: + text: "# scaffolds 79" + Nx Plot: + asserts: + has_size: + value : 57000 + delta: 5000 + Size Plot: + asserts: + has_size: + value : 84000 + delta: 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It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5) + +## Inputs + +1. Genomescope model parameters [txt] (Generated by the k-mer profiling workflow) +1. Hifi long reads - trimmed [fastq] (Generated by Cutadapt in the contigging workflow) +2. Assembly to purge (e.g. hap1) [fasta] (Generated by the contigging workflow) +3. K-mer database [meryldb] (Generated by the k-mer profiling workflow) +4. Estimated Genome Size [txt] +5. Assembly to leave alone (used for merqury statistics) (e.g. hap2) [fasta] (Generated by the contigging workflow) +6. Name of un-altered assembly +7. Name of purged assembly + + +## Outputs + +1. Haplotype 1 purged assembly (Fasta and gfa) +2. Haplotype 2 purged assembly (Fasta and gfa) +3. QC: BUSCO report for both assemblies +4. QC: Merqury report for both assemblies +5. QC: Assembly statistics for both assemblies +6. QC: Nx plot for both assemblies +7. QC: Size plot for both assemblies \ No newline at end of file