Merge branch 'master' of https://github.com/minoda-lab/universc (377692f9) · Commits · github_fork / Universc

.github/workflows/docker-test-build.yml

+1 −1

Original line number	Diff line number	Diff line
		@@ -32,4 +32,4 @@ jobs:
		- name: Status
		run: echo "build complete"
		- name: Call functions
		run: docker run universc:latest bash /universc/test/test_call.sh
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}universc:latest bash /universc/test/test_call.sh

launch_universc.sh

+8 −8

Original line number	Diff line number	Diff line
		@@ -1176,36 +1176,36 @@ for key in ${keys[@]}; do
		rename -f "s/_${readkey}.(.*).gz/_${readkey}_001\.\$1.gz/g" ${read}
		fi
		if [[ -f $(find $(dirname ${read}) -name $(basename ${read})'*.fastq') ]]; then
		rename -f "s/_${readkey}.(.)/_${readkey}_001\.\$1/" ${read}.fastq
		rename -f "s/_${readkey}\.(.)/_${readkey}_001\.\$1/" ${read}.fastq
		fi
		if [[ -f $(find $(dirname ${read}) -name $(basename ${read})'*.fq') ]]; then
		rename -f "s/_${readkey}.(.)/_${readkey}_001\.\$1/" ${read}.fq
		rename -f "s/_${readkey}\.(.)/_${readkey}_001\.\$1/" ${read}.fq
		fi
		if [[ ${read} == *.fastq ]]; then
		rename -f "s/_${readkey}(.*).fastq/_${readkey}_001\.fastq/" ${read} ${read}.gz
		rename -f "s/_${readkey}*\.fastq/_${readkey}_001\.fastq/" ${read} ${read}.gz
		fi
		if [[ ${read} == *.fq ]]; then
		rename -f "s/_${readkey}(.*).fq/_${readkey}_001\.fq/" ${read}
		rename -f "s/_${readkey}*\.fq/_${readkey}_001\.fq/" ${read}
		fi
		#update file variable
		if [[ ${read} == .gz ]] \|\| [[ ${read} == .fastq ]] \|\| [[ ${read} == *.fq ]] \|\| [[ -f ${read} ]]; then
		#assumes read name already contains . in file extension
		read=`echo $read \| sed -e "s/_${readkey}.*\./_${readkey}_001\./g"`
		read=`echo $read \| sed -e "s/_${readkey}*\./_${readkey}_001\./g"`
		else
		#replace everything after read key (R1, R2, I1, I2) with 001 suffix (detects file later)
		rename -f "s/_${readkey}.*/_${readkey}_001/g" ${read}
		read=`echo $read \| sed -e "s/_${readkey}.*/_${readkey}_001/g"`
		read=`echo $read \| sed -e "s/_${readkey}*/_${readkey}_001/g"`
		fi
		#remove characters after read key (R1, R2, I1, I2) required as above
		if [[ ${read} != _${readkey}_001. ]] && [[ ${read} != . ]]; then
		rename -f "s/_${readkey}_*\./_${readkey}_001\./" ${read}
		read=`echo $read \| sed -e "s/_${readkey}.*\./_${readkey}_001\./g"`
		read=`echo $read \| sed -e "s/_${readkey}*\./_${readkey}_001\./g"`
		elif [[ ${read} != _${readkey}_001 ]] \|\| [[ ${read} != _${readkey}*00#1 ]]; then
		rename -f "s/_${readkey}*_001/_${readkey}_001/" ${read#}
		read=`echo $read \| sed -e "s/_${readkey}*_001/_${readkey}_001/g"`
		fi
		if [[ ${read} == _${readkey}__001.* ]]; then
		rename -f "s/_${readkey}.*_001\./_${readkey}_001\./" ${read}
		rename -f "s/_${readkey}*_001\./_${readkey}_001\./" ${read}
		read=`echo $read \| sed -e "s/_${readkey}*_001\./_${readkey}_001\./g"`
		fi

test/run_tests_10x_local.sh

+3 −3

Original line number	Diff line number	Diff line
		@@ -69,7 +69,7 @@ fi
		cellranger count --id="tiny-count-v3" \
		--fastqs="test/shared/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--jobmode "local" --localcores 1
		--jobmode "local" --localcores 2 --localmem 4
		if [[ -d tiny-count-v2 ]]; then
		rm -rf tiny-count-v2
		fi
		@@ -82,7 +82,7 @@ fi
		cellranger count --id="tiny-count-v2" \
		--fastqs="test/shared/cellranger-tiny-fastq/1.2.0/" --sample="" --chemistry="threeprime" \
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0" \
		--jobmode "local" --localcores 1
		--jobmode "local" --localcores 2 --localmem 4

		# call convert on 10x with multiple lanes
		if [[ -d test-10x-v3 ]]; then
		@@ -102,7 +102,7 @@ bash launch_universc.sh --id "test-10x-v3" --technology "10x" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--file "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \
		"test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002" \
		--jobmode "local" --localcores 1
		--jobmode "local" --localcores 2 --localmem 4

		# compress all input files
		if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

test/run_tests_dropseq_local.sh

+1 −1

Original line number	Diff line number	Diff line
		@@ -42,7 +42,7 @@ bash launch_universc.sh --id "test-dropseq" --technology "nadia" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--read1 "test/shared/dropseq-test/SRR1873277_Sample1_R1" \
		--read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2" \
		--jobmode "local" --localcores 1
		--jobmode "local" --localcores 2 --localmem 4

		# reset test data (compress)
		if [[ -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq ]]; then

test/run_tests_icell8_local.sh

+2 −2

Original line number	Diff line number	Diff line
		@@ -40,7 +40,7 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCe
		--read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R1_001.fastq" \
		--read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R2_001.fastq" \
		--barcodefile "test/shared/icell8-test/WellList.txt" \
		--jobmode "local" --localcores 1
		--jobmode "local" --localcores 2 --localmem 4
		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
		@@ -61,7 +61,7 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel
		--read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" \
		--read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \
		--barcodefile "test/shared/icell8-test/WellList.txt" \
		--jobmode "local" --localcores 1
		--jobmode "local" --localcores 2 --localmem 4
		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

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