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Commit d6c6cedf authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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correct bug counts

parent 1ed94044
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......@@ -236,7 +236,6 @@ if config["feature_counts"]["do"]:
feature_counts_input = "02-Mapping/{MAP}/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam"
feature_counts_output_count = "03-Counting/{MAP}/{SAMPLE}_{REF}_feature.out"
feature_counts_output_gene_count = "03-Counting/{MAP}/{SAMPLE}_{REF}_feature_cut.out"
feature_counts_gff = config['genome']['gff_file']
feature_counts_logs_err = "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.err"
feature_counts_logs_out = "03-Counting/logs/{MAP}/{SAMPLE}_{REF}_feature.out"
......
......@@ -33,17 +33,17 @@ rule feature_counts:
singularity:
"rnaflow.img"
params:
mapp = feature_counts_options,
input = feature_counts_optional_input
mapp = feature_counts_options
log:
feature_counts_log
err = feature_counts_logs_err,
out = feature_counts_logs_out
threads:
feature_counts_threads
envmodules:
"subread/1.6.1"
shell:
"""
featureCounts -T {threads} {params.mapp} -a {input.gff} -o {output} {input.bam} {params.input} 2> {log}
featureCounts -T {threads} {params.mapp} -a {input.gff} -o {output} {input.bam} > {log.out} 2> {log.err}
"""
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