Phaseimpute template update and pass first test #5
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And remove this step from phaseimpute and put it in the utils_phaseimpute subworkflow
Improve schema and config Add map channel
assets/chr_rename_add.txt
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look like it's just adding chr to the chromosome, any other way to do so, that doesn't rely on such a list?
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That could be a module using a fai ?
assets/chr_rename_del.txt
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similar question for this one
Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
Co-authored-by: Maxime U Garcia <[email protected]>
| @@ -22,7 +22,7 @@ params { | |||
| map = "/groups/dog/llenezet/test-datasets/data/genetic_maps.b38/chr21.b38.gmap.gz" | |||
| genome = "GRCh38" | |||
| fasta = "/groups/dog/llenezet/script/phaseimpute/data/genome.fa" | |||
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I feel like these path are a bit too specific to your system, but that can be fix later on, just don't forget about it, otherwise the megatests will fail badly
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For sure.
I'm currently working on the creation of such dataset
| }, | ||
| "bedtools/makewindows": { | ||
| "branch": "master", | ||
| "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", | ||
| "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", | ||
| "installed_by": ["vcf_phase_shapeit5"] | ||
| }, | ||
| "custom/dumpsoftwareversions": { |
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@maxulysse what do you mean by not deleted yet ?
| - def annotations_file = annotations ? "--annotations ${annotations}" : '' | ||
| + def header_file = header_lines ? "--header-lines ${header_lines}" : '' | ||
| + def annotations_file = annotations ? "--annotations ${annotations}" : '' | ||
| + def rename_chr_cmd = rename_chr ? "--rename-chrs ${rename_chr}" : '' |
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oh I see, this is where it's coming from
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Maybe that can be added to the module then
Update fasta use with genome
Phaseimpute template update and pass first test
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nf-core lint).nf-test test main.nf.test -profile test,docker).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).