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feat: make sending lab column in rki report csv adjustable via config file #492

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merged 4 commits into from
Mar 1, 2022
Merged

feat: make sending lab column in rki report csv adjustable via config file #492

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5dd2313
added parameter in order to make the sending lab column in rki report…
lenakinzel Feb 23, 2022
4e47244
added the date of the current run to the generate_output.smk to refil…
lenakinzel Mar 1, 2022
3d98552
Merge branch 'master' into make-sending-lab-column-adjustable
lenakinzel Mar 1, 2022
924d4c7
Merge branch 'master' into make-sending-lab-column-adjustable
thomasbtf Mar 1, 2022
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2 changes: 2 additions & 0 deletions .tests/config/config.yaml
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Expand Up @@ -23,6 +23,8 @@ virus-reference-genome:
human-genome-download-path:
- ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GCA_000001405.28_GRCh38.p13_genomic.fna.gz

sending_lab_number: 10259

data-handling:
# flag for using the following data-handling structure
# True: data-handling structure is used as shown below
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2 changes: 2 additions & 0 deletions config/config.yaml
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Expand Up @@ -11,6 +11,8 @@ virus-reference-genome:
human-genome-download-path:
- ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GCA_000001405.28_GRCh38.p13_genomic.fna.gz

sending_lab_number: 10259

data-handling:
# flag for using the following data-handling structure
# True: data-handling structure is used as shown below
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5 changes: 5 additions & 0 deletions workflow/rules/generate_output.smk
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Expand Up @@ -4,6 +4,9 @@
# except according to those terms.


configfile: "config/config.yaml"


rule masking:
input:
bamfile="results/{date}/mapped/ref~{reference}-{sample}/{sample}.bam",
Expand Down Expand Up @@ -107,6 +110,8 @@ rule high_quality_genomes_report:
),
params:
includeflag=get_include_flag_for_date,
sending_lab_number=config["sending_lab_number"],
date_draw=lambda wildcards: wildcards.date,
seq_type=lambda wildcards: get_assemblies_for_submission(
wildcards, "accepted samples technology"
),
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4 changes: 2 additions & 2 deletions workflow/scripts/generate-high-quality-report.py
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Expand Up @@ -51,8 +51,8 @@
# Creating csv-table
csv_table = pd.DataFrame(
{
"SENDING_LAB": 10259,
"DATE_DRAW": "",
"SENDING_LAB": snakemake.params.sending_lab_number,
"DATE_DRAW": snakemake.params.date_draw,
"SEQ_TYPE": snakemake.params.seq_type,
"SEQ_REASON": "N",
"SAMPLE_TYPE": "s001",
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