changed sort temp directory to working folder (5daad875) · Commits · Chaos / Cutandrun

conf/modules.config

+3 −3

Original line number	Diff line number	Diff line
		@@ -277,7 +277,7 @@ params {
		args = "-f 1,2,6"
		suffix = ".frags"
		ext = "bed"
		command = "\| sort -k1,1 -k2,2n -k3,3n"
		command = "\| sort -T '.' -k1,1 -k2,2n -k3,3n"
		publish_dir = "03_peak_calling/06_fragments"
		}

		@@ -287,12 +287,12 @@ params {
		ext = "bed"
		publish_dir = "03_peak_calling/06_fragments"
		command = "'{print \$1, int((\$2 + \$3)/(2w))w + w/2, FILENAME}'"
		command2 = "\| sort -k1,1V -k2,2n \| uniq -c \| awk -v OFS=\"\\t\" '{print \$2, \$3, \$1, \$4}' \| sort -k1,1V -k2,2n"
		command2 = "\| sort -T '.' -k1,1V -k2,2n \| uniq -c \| awk -v OFS=\"\\t\" '{print \$2, \$3, \$1, \$4}' \| sort -T '.' -k1,1V -k2,2n"
		}

		"samtools_frag_len" {
		args = "-F 0x04"
		args2 = "awk -F'\\t' 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs(\$9)}' \| sort \| uniq -c \| awk -v OFS=\"\\t\" '{print \$2, \$1/2}'"
		args2 = "awk -F'\\t' 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs(\$9)}' \| sort -T '.' \| uniq -c \| awk -v OFS=\"\\t\" '{print \$2, \$1/2}'"
		suffix = ".frag_len"
		publish_dir = "03_peak_calling/06_fragments"
		}

+1 −1

Original line number	Diff line number	Diff line
		@@ -37,6 +37,6 @@ process SORT {
		String input_files = input.join(" ")

		"""
		sort $options.args $input_files > ${prefix}.sort.${ext}
		sort -T '.' $options.args $input_files > ${prefix}.sort.${ext}
		"""
		}