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check every bam file has an index #77

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Nov 23, 2015
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check every bam file has an index #77

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6 changes: 5 additions & 1 deletion needlestack.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -110,7 +110,11 @@ try { assert file(params.bam_folder).exists() : "\n WARNING : input BAM folder n
assert file(params.bam_folder).listFiles().findAll { it.name ==~ /.*bam/ }.size() > 0 : "BAM folder contains no BAM"
if (file(params.bam_folder).exists()) {
if (file(params.bam_folder).listFiles().findAll { it.name ==~ /.*bam/ }.size() < 10) {println "\n WARNING : BAM folder contains less than 10 BAM, regression will not be performed."}
else if (file(params.bam_folder).listFiles().findAll { it.name ==~ /.*bam/ }.size() < 20) {println "\n WARNING : BAM folder contains less than 20 BAM, method accuracy not warranted."} }
else if (file(params.bam_folder).listFiles().findAll { it.name ==~ /.*bam/ }.size() < 20) {println "\n WARNING : BAM folder contains less than 20 BAM, method accuracy not warranted."}
bamID = file(params.bam_folder).listFiles().findAll { it.name ==~ /.*bam/ }.collect { it.getName() }.collect { it.replace('.bam','') }
baiID = file(params.bam_folder).listFiles().findAll { it.name ==~ /.*bam.bai/ }.collect { it.getName() }.collect { it.replace('.bam.bai','') }
assert baiID.containsAll(bamID) : "check that every bam file has an index (.bam.bai)"
}
assert (params.min_dp > 0) : "minimum coverage must be higher than 0 (--min_dp)"
assert (params.max_DP > 1) : "maximum coverage before downsampling must be higher than 1 (--max_DP)"
assert (params.min_ao > 0) : "minimum alternative reads must be higher than 0 (--min_ao)"
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