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feat: rule and script bed_to_bedpe (#447)
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* Rule and script bed_to_bedpe

* Added bed to config, changed rule input paths

* Bed files can be downloaded via url in config

* fmt
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@AKBrueggemann
AKBrueggemann authored Feb 2, 2022
1 parent c18f241 commit 3022eab
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2 changes: 1 addition & 1 deletion .tests/config/config.yaml
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Expand Up @@ -65,7 +65,7 @@ preprocessing:
# for more information
artic-primer-version: 3
# path to amplicon primers in bedpe format for hard-clipping on paired end files (illumina)
amplicon-primers: "resources/primer.bedpe"
amplicon-primers: "resources/nCoV-2019.primer.bed"
# GenBank accession of reference sequence of the amplicon primers
amplicon-reference: "MN908947"

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218 changes: 218 additions & 0 deletions .tests/resources/nCoV-2019.primer.bed
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4 changes: 2 additions & 2 deletions config/config.yaml
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Expand Up @@ -52,8 +52,8 @@ preprocessing:
# https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4
# for more information
artic-primer-version: 3
# path to amplicon primers in bedpe format for hard-clipping on paired end files (illumina)
amplicon-primers: "resources/primer.bedpe"
# path to amplicon primers in bed format for hard-clipping on paired end files (illumina) or url to file that should be downloaded
amplicon-primers: "resources/nCoV-2019.primer.bed"
# GenBank accession of reference sequence of the amplicon primers
amplicon-reference: "MN908947"

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