Commit 5ff69f92 authored by Raphael Müller's avatar Raphael Müller
Browse files

typo in ccs file

parent f9ee0bf2
......@@ -330,7 +330,7 @@ if (bamAvailable) {
script:
"""
minimap2 $minimapPacbioCCSOptions -x asm20 -a -t ${task.cpus} $gen $pb 2> \
${prefix}_minimap_pb${task.index}.err | samtools view -1 -b - > ${prefix}.pb${task.index}.bam
${prefix}_minimap_pb${task.index}.err | samtools view -1 -b - > ${prefix}.pb_ccs${task.index}.bam
"""
} // process pacbioCCSMapping
......
......@@ -4,8 +4,8 @@ NAME = "clrccs"
rule assembly_pacbio_clr_ccs:
input:
assembly = ASSEMBLY,
clr = "data_prep/pbsim_clr_30.fastq",
ccs = "data_prep/pbsim_ccs_30.fastq",
clr = "data_prep/pbsim_clr_5.fastq",
ccs = "data_prep/pbsim_ccs_5.fastq",
output:
sort_stats_pb = multiext(OF+NAME+".pb.sort_stats/", "genome_results.txt", "qualimapReport.html"),
pacbio_clr = multiext(OF+NAME+".pb","1.bam",".bam",*multiext(".sort.bam","",*multiext(".cov-hist","",".pdf"), ".stats",".stats.err"),*multiext(".sort_stats_bamqc.","err","log")) + [OF+NAME+"_minimap_pb1.err"],
......
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