diff --git a/snakemake/process_data/Snakefile b/snakemake/process_data/Snakefile index 0d869f4f1db37782a1e6725df2f733426c995041..5e714a14e51a045764c1995a2a291ffdda763242 100644 --- a/snakemake/process_data/Snakefile +++ b/snakemake/process_data/Snakefile @@ -27,7 +27,7 @@ rule clip_reads: v = "-v", n = "-n", l = "20", - adapter = "GATCGGAAGAGCACA", #lambda wildcards: config[wildcards.sample]['adapter'], + adapter = lambda wildcards: config[wildcards.sample]['adapter'], z = "-z" log: os.path.join(config["local_log"], "clip_reads_{sample}.log") diff --git a/snakemake/process_data/config.yaml b/snakemake/process_data/config.yaml index f3b40e9ab620f617b5e8ec6d585c84767ef498ec..25adcf21a79af2ad5e389e414f9b02a04efd3547 100644 --- a/snakemake/process_data/config.yaml +++ b/snakemake/process_data/config.yaml @@ -18,9 +18,9 @@ ############################################################################## input_dir: "samples" input_reads_pattern: ".fastq.gz" - sample: ["example"] #, "example2", "SRR1536304", "SRR1536305"] - example: {adapter: "GATCGGAAGAGCACA", minimum_quality: 20, quality_type: 33} -# example2: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 64} -# SRR1536304: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33} -# SRR1536305: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33} + sample: ["example", "example2", "SRR1536304", "SRR1536305"] + example: {adapter: GATCGGAAGAGCACA, minimum_quality: 20, quality_type: 33} + example2: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 64} + SRR1536304: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33} + SRR1536305: {adapter: CTGTAGGCACCATCA, minimum_quality: 20, quality_type: 33} ...