Commit 0efc60de authored by van den Berg's avatar van den Berg
Browse files

Snakemake 5.19.3 has 'insert' as a reserved word

parent 50e50edd
......@@ -457,7 +457,7 @@ rule multiple_metrics:
prefix = "{sample}/bams/{sample}",
output:
alignment = "{sample}/bams/{sample}.alignment_summary_metrics",
insert = "{sample}/bams/{sample}.insert_size_metrics"
insertMetrics = "{sample}/bams/{sample}.insert_size_metrics"
container: containers["picard"]
shell: "picard CollectMultipleMetrics "
"I={input.bam} O={params.prefix} "
......@@ -530,7 +530,7 @@ rule multiqc:
output:
html = "multiqc_report/multiqc_report.html",
insert = "multiqc_report/multiqc_data/multiqc_picard_insertSize.json",
insertSize = "multiqc_report/multiqc_data/multiqc_picard_insertSize.json",
AlignmentMetrics = "multiqc_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.json",
DuplicationMetrics = "multiqc_report/multiqc_data/multiqc_picard_dups.json",
HsMetrics = "multiqc_report/multiqc_data/multiqc_picard_HsMetrics.json" if "baitsfile" in config else []
......@@ -544,7 +544,7 @@ rule merge_stats:
cols = expand("{sample}/{sample}.stats.json",
sample=config['samples']),
mpy = config["merge_stats"],
insertSize = rules.multiqc.output.insert,
insertSize = rules.multiqc.output.insertSize,
AlignmentMetrics = rules.multiqc.output.AlignmentMetrics,
DuplicationMetrics = rules.multiqc.output.DuplicationMetrics,
HsMetrics = rules.multiqc.output.HsMetrics
......
Subproject commit f9eafd882170e7cca228d2bbf580e28f7790ced6
Subproject commit 4dd69175adc5360cadea79feac6386ccef41d923
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