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feat: add additional primer file for ont #589

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feat: add additional primer file for ont #589

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e2edf36
add additional primer file for ont
alethomas Mar 2, 2023
206815e
change config scheme
alethomas Mar 2, 2023
90eff73
fix path
alethomas Mar 2, 2023
c253aa8
fix schema structure
johanneskoester Mar 2, 2023
fecd188
fix config structure for testcase
johanneskoester Mar 2, 2023
1ed083d
change also .tests/config
alethomas Mar 3, 2023
3a24f9c
Merge branch 'master' into feat/multiple-primer-files
alethomas Nov 15, 2023
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3 changes: 2 additions & 1 deletion .tests/config/config.yaml
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Expand Up @@ -77,7 +77,8 @@ 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/nCoV-2019.primer.bed"
amplicon-primers:
illumina: "resources/nCoV-2019.primer.bed"
# GenBank accession of reference sequence of the amplicon primers
amplicon-reference: "MN908947"

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4 changes: 3 additions & 1 deletion config/config.yaml
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Expand Up @@ -63,7 +63,9 @@ preprocessing:
# for more information
artic-primer-version: 3
# 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"
amplicon-primers:
ont: "resources/nCoV-2019.primer.bed"
illumina: "resources/nCoV-2019.primer.bed"
# GenBank accession of reference sequence of the amplicon primers
amplicon-reference: "MN908947"

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4 changes: 2 additions & 2 deletions workflow/rules/long_read.smk
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Expand Up @@ -56,7 +56,7 @@ rule nanofilt:

rule downsample_and_trim_raw:
input:
primer=config["preprocessing"]["amplicon-primers"],
primer=config["preprocessing"]["amplicon-primers"]["ont"],
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reads="results/{date}/filtered/nanofilt/{sample}.fastq",
ref_genome="resources/genomes/main.fasta",
output:
Expand Down Expand Up @@ -121,7 +121,7 @@ rule canu_correct:

rule clip_adbc_corrected:
input:
primer=config["preprocessing"]["amplicon-primers"],
primer=config["preprocessing"]["amplicon-primers"]["ont"],
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reads="results/{date}/corrected/{sample}/{sample}.correctedReads.fasta",
ref_genome="resources/genomes/main.fasta",
output:
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2 changes: 1 addition & 1 deletion workflow/rules/read_clipping.smk
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Expand Up @@ -22,7 +22,7 @@ rule samtools_sort:

rule bed_to_bedpe:
input:
check_bed_for_URL(config["preprocessing"]["amplicon-primers"]),
check_bed_for_URL(config["preprocessing"]["amplicon-primers"]["illumina"]),
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output:
"resources/primer.bedpe",
log:
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10 changes: 8 additions & 2 deletions workflow/schemas/config.schema.yaml
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Expand Up @@ -67,8 +67,14 @@ properties:
type: integer
description: only for Oxford Nanopore data. ARTIC primer version to clip from reads
amplicon-primers:
type: string
description: path to amplicon primers in bedpe format for hard-clipping on paired end files (illumina)
type: object
properties:
ont:
type: string
description: path to amplicon primers in bed format for hard-clipping on single end files (Oxford Nanopore)
illumina:
type: string
description: path to amplicon primers in bed format for hard-clipping on paired end files (Illumina)
amplicon-reference:
type: string
description: GenBank accession of reference sequence of the amplicon primers
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