add pigz dependency for docker (080aeea0) · Commits · github_fork / Universc

Dockerfile

+1 −0

Original line number	Diff line number	Diff line
		@@ -8,6 +8,7 @@ RUN apt-get update \
		git-lfs \
		make \
		gzip \
		pigz \
		rename

		RUN apt-get install -y \

test/run_tests_icell8.sh

+19 −7

Original line number	Diff line number	Diff line
		@@ -21,16 +21,16 @@ fi
		unpigz -k test/shared/icell8-test/72618_KU812*fastq.gz

		if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*
		fi
		if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*
		fi
		if [ -f test/shared/icell8-test/72618_KU812_S2_L002_R1_001.fastq ]; then
		rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R1_001.fastq
		rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R1_001.fastq*
		fi
		if [ -f test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq ]; then
		rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq
		rename -n "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq*
		fi
		if [ -d test-icell8-72618-KU812-2-lanes ];then
		rm -rf test-icell8-72618_KU812-2-lanes
		@@ -42,10 +42,16 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCe
		--barcodefile "test/shared/icell8-test/WellList.txt" \
		--jobmode "local"
		if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*
		fi
		if [ -f test/shared/icell8-test/KU812_S1_L001_R2_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq
		if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq*
		fi
		if [ -f test/shared/icell8-test/72618_KU812_S1_L002_R1_001.fastq ]; then
		rename "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R1_001.fastq*
		fi
		if [ -f test/shared/icell8-test/72618_KU812_S1_L002_R2_001.fastq ]; then
		rename "s/_S2_L002/_L002/" test/shared/icell8-test/72618_KU812_S2_L002_R2_001.fastq*
		fi
		if [ -d test-icell8-72618_KU812-1-lane ]; then
		rm -rf test-icell8-72618_KU812-1-lane
		@@ -56,3 +62,9 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel
		--read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \
		--barcodefile "test/shared/icell8-test/WellList.txt" \
		--jobmode "local"
		if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*
		fi
		if [ -f test/shared/icell8-test/KU812_S1_L001_R2_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R2_001.fastq*
		fi

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