fix: different names for downloads to avoid name clashes (#71)

* fix: different names for downloads to avoid name clashes * lint: fix param prefix * lint: deploy non-file parameter --------- Co-authored-by: Yannic Eising <yeising@students.uni-mainz.de>
snakemake-workflows · Aug 22, 2024 · 756ba5b · 756ba5b
1 parent 1b50d39
commit 756ba5b
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/workflow/rules/quantification.smk b/workflow/rules/quantification.smk
@@ -9,7 +9,7 @@ rule count_reads:
     output:
         tsv="counts/{sample}_salmon/quant.sf",
     params:
-        tsv_dir="counts/{sample}_salmon",
+        outdir=lambda wildcards, ouput: output[0][:-9],
         libtype=config["salmon_libtype"],
     log:
         "logs/salmon/{sample}.log",
@@ -18,7 +18,7 @@ rule count_reads:
     shell:
         """
         salmon --no-version-check quant --ont -p {resources.cpus_per_task} \
-        -t {input.trs} -l {params.libtype} -a {input.bam} -o {params.tsv_dir} 2> {log}
+        -t {input.trs} -l {params.libtype} -a {input.bam} -o {params.outdir} 2> {log}
         """
 
 

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
@@ -14,9 +14,9 @@ rule get_genome:
         "../envs/env.yml"
     shell:
         """
-        curl -o data.zip https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/{params.accession}/download?include_annotation_type=GENOME_FASTA &> {log};
-        unzip -p data.zip ncbi_dataset/data/{params.accession}/*.fna > references/genomic.fa 2> {log};
-        rm data.zip &> {log}
+        curl -o data_genome.zip https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/{params.accession}/download?include_annotation_type=GENOME_FASTA &> {log};
+        unzip -p data_genome.zip ncbi_dataset/data/{params.accession}/*.fna > references/genomic.fa 2> {log};
+        rm data_genome.zip &> {log}
         """
 
 
@@ -31,7 +31,7 @@ rule get_annotation:
         "../envs/env.yml"
     shell:
         """
-        curl -o data.zip https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/{params.accession}/download?include_annotation_type=GENOME_GFF &> {log};
-        unzip -p data.zip ncbi_dataset/data/{params.accession}/*.gff > references/genomic.gff 2> {log};
-        rm data.zip &> {log}
+        curl -o data_annotation.zip https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/{params.accession}/download?include_annotation_type=GENOME_GFF &> {log};
+        unzip -p data_annotation.zip ncbi_dataset/data/{params.accession}/*.gff > references/genomic.gff 2> {log};
+        rm data_annotation.zip &> {log}
         """