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Fix genome size #146

Merged
merged 28 commits into from
Sep 25, 2023
Merged

Fix genome size #146

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25a27c6
Adding pretext ingestion docs
DLBPointon Sep 21, 2023
c4620c9
Update docs/usage.md
DLBPointon Sep 21, 2023
83c3f67
Fix for custom-getchromsizes
DLBPointon Sep 21, 2023
991ebca
Merge branch 'More-docs' of https://github.com/sanger-tol/treeval int…
DLBPointon Sep 21, 2023
0a44839
Removing <button type="button" class="collapsible">Open Collapsible</…
DLBPointon Sep 21, 2023
dc17a30
fix_genome_size
yumisims Sep 21, 2023
8fdd360
Updated docs to a singular file, i've used alot of HTML to make sure …
DLBPointon Sep 22, 2023
c7dfaaa
Deletion
DLBPointon Sep 22, 2023
f4ddbd9
Deletion
DLBPointon Sep 22, 2023
801c21a
Prettier
DLBPointon Sep 22, 2023
3505c9e
Adding pretext ingestion docs
DLBPointon Sep 21, 2023
37e79e9
Update docs/usage.md
DLBPointon Sep 21, 2023
fac87f2
Fix for custom-getchromsizes
DLBPointon Sep 21, 2023
d9946a5
Removing <button type="button" class="collapsible">Open Collapsible</…
DLBPointon Sep 21, 2023
d7f365f
Updated docs to a singular file, i've used alot of HTML to make sure …
DLBPointon Sep 22, 2023
af213ef
Deletion
DLBPointon Sep 22, 2023
877d9f0
Deletion
DLBPointon Sep 22, 2023
c7f77c8
Prettier
DLBPointon Sep 22, 2023
298e247
Merge branch 'More-docs' of https://github.com/sanger-tol/treeval int…
DLBPointon Sep 22, 2023
c39d28d
Regular markdown should work
muffato Sep 25, 2023
02d10f5
More changes
muffato Sep 25, 2023
750b0ec
More changes
muffato Sep 25, 2023
e0c8621
More changes (and prettier)
muffato Sep 25, 2023
7b58017
Changed genomic_alignment_data
muffato Sep 25, 2023
29e6598
Update usage.md
DLBPointon Sep 25, 2023
3d5ea17
Merge pull request #149 from sanger-tol/mm49_docs_reformat
DLBPointon Sep 25, 2023
5b4bb92
Merge branch 'More-docs' into fix_genome_size
DLBPointon Sep 25, 2023
580ee1c
Merge branch 'More-docs' into fix_genome_size
DLBPointon Sep 25, 2023
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2 changes: 1 addition & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ process {

// Files to be uploaded to the TreeVal JBrowse2 instance
// .genome, .gz.{tbi|csi}, .bigBed, .bigWig, .paf
withName: 'GENERATE_GENOME_FILE|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED|UCSC_BEDGRAPHTOBIGWIG|.*:.*:SYNTENY:MINIMAP2_ALIGN|.*:.*:GENERATE_GENOME:CUSTOM_GETCHROMSIZES' {
withName: 'GENERATE_GENOME_FILE|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED|UCSC_BEDGRAPHTOBIGWIG|.*:.*:SYNTENY:MINIMAP2_ALIGN|.*:.*:GENERATE_GENOME:GNU_SORT' {
publishDir = [
path: { "${params.outdir}/treeval_upload" },
mode: params.publish_dir_mode,
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213 changes: 0 additions & 213 deletions docs/genealignmentsynteny.md
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56 changes: 0 additions & 56 deletions docs/pacbio.md
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