diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3047686ceae25183ac16e0b5eddce72f31631e12..88100ccbe67cdd395f72fe81eba64d31f273c754 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -156,7 +156,7 @@ alignData: - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o 16-WJRA_1M.se.bam 16-WJRA_1M.se.sam - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o 16-WJRA_1M.se.sorted.bam 16-WJRA_1M.se.bam - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b 16-WJRA_1M.se.sorted.bam 16-WJRA_1M.se.sorted.bam.bai - - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz 16-WJRA_1M.pe.unal.gz -S 16-WJRA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/16-WJRA_1M.pe_R1_val_1.fq.gz -2 ./test_data/fastq/small/16-WJRA_1M.pe_R2_val_2.fq.gz --summary-file 16-WJRA_1M.pe.alignSummary.txt --new-summary + - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 -p 20 --add-chrname --un-gz 16-WJRA_1M.pe.unal.gz -S 16-WJRA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/16-WJRA_1M.pe_val_1.fq.gz -2 ./test_data/fastq/small/16-WJRA_1M.pe_val_2.fq.gz --summary-file 16-WJRA_1M.pe.alignSummary.txt --new-summary - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o 16-WJRA_1M.pe.bam 16-WJRA_1M.pe.sam - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o 16-WJRA_1M.pe.sorted.bam 16-WJRA_1M.pe.bam - singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b 16-WJRA_1M.pe.sorted.bam 16-WJRA_1M.pe.sorted.bam.bai diff --git a/workflow/tests/test_alignReads.py b/workflow/tests/test_alignReads.py index 11f0f3d0d09236a3f3494a2c851fb4294f2a1323..d1242055a99b4a21a47b9acec9c943bed5443362 100644 --- a/workflow/tests/test_alignReads.py +++ b/workflow/tests/test_alignReads.py @@ -12,18 +12,18 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.alignData def test_alignData_se(): assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.unal.gz')) + data_output_path, '16-WJRA_1M.se.unal.gz')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.bam')) + data_output_path, '16-WJRA_1M.se.sorted.bam')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.bam.bai')) + data_output_path, '16-WJRA_1M.se.sorted.bam.bai')) @pytest.mark.alignData def test_alignData_pe(): assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.pe.unal.gz')) + data_output_path, '16-WJRA_1M.pe.unal.gz')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.pe.sorted.bam')) + data_output_path, '16-WJRA_1M.pe.sorted.bam')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.pe.sorted.bam.bai')) + data_output_path, '16-WJRA_1M.pe.sorted.bam.bai')) diff --git a/workflow/tests/test_dataQC.py b/workflow/tests/test_dataQC.py index 55df66deaeda6dac18ea26455dd1e3948ceb28ba..072253a5b856fac4ce0648793bea8c3743efcf13 100644 --- a/workflow/tests/test_dataQC.py +++ b/workflow/tests/test_dataQC.py @@ -12,9 +12,9 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.dataQC def test_dataQC(): assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_1M.se.sorted.deduped.tin.xls')) + test_output_path, '16-WJRA_1M.se.sorted.deduped.tin.xls')) assert countLines(os.path.join(test_output_path, - 'Q-Y5F6_1M.se.sorted.deduped.tin.xls')) + '16-WJRA_1M.se.sorted.deduped.tin.xls')) def countLines(fileName): diff --git a/workflow/tests/test_dedupReads.py b/workflow/tests/test_dedupReads.py index 89fc2b10fa4db847ccc16d5cce664bf551b29ee3..dee270c13aaa4e199a81ad4f1ec63c60b7d09ee5 100644 --- a/workflow/tests/test_dedupReads.py +++ b/workflow/tests/test_dedupReads.py @@ -12,18 +12,18 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.dedupData def test_dedupData(): assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.bam')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.bam.bai')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.bam.bai')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.chr8.bam')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr8.bam.bai')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.chr8.bam.bai')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.chr4.bam')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chr4.bam.bai')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.chr4.bam.bai')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.chrY.bam')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.sorted.deduped.chrY.bam.bai')) + data_output_path, '16-WJRA_1M.se.sorted.deduped.chrY.bam.bai')) diff --git a/workflow/tests/test_fastqc.py b/workflow/tests/test_fastqc.py index 07e76108fbfc92f945060d8e5d1e1ea8f74e6a4a..5a22a1bd412be2232393cb6c1562376bcfc84e8f 100644 --- a/workflow/tests/test_fastqc.py +++ b/workflow/tests/test_fastqc.py @@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.fastqc def test_fastqc(): assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_1M.R1_fastqc.zip')) + test_output_path, '16-WJRA_1M.R1_fastqc.zip')) diff --git a/workflow/tests/test_getBag.py b/workflow/tests/test_getBag.py index 23bfc0ea50c260a2f5c4cbf62321c066b5743ac2..66f233a20cdb3012eb2b42d7e962b37fe33155d7 100644 --- a/workflow/tests/test_getBag.py +++ b/workflow/tests/test_getBag.py @@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.getBag def test_getBag(): assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_inputBag.zip')) + test_output_path, '16-WJRA_inputBag.zip')) diff --git a/workflow/tests/test_getData.py b/workflow/tests/test_getData.py index 596a120abe904eac8f3e0ad871c9f8c03a6cba5f..926f6f9d6c9319e16d40e4cbbc17eaa14f9ee315 100644 --- a/workflow/tests/test_getData.py +++ b/workflow/tests/test_getData.py @@ -12,6 +12,6 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.getData def test_getData(): assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_inputBag/bagit.txt')) + test_output_path, '16-WJRA_inputBag/bagit.txt')) assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_inputBag/data/assets/Study/Q-Y4GY/Experiment/Q-Y4DP/Replicate/Q-Y5F6/mMARIS_Six2-#3.gene.rpkm.txt')) + test_output_path, '16-WJRA_inputBag/data/assets/Study/Q-Y4GY/Experiment/Q-Y4DP/Replicate/16-WJRA/mMARIS_Six2-#3.gene.rpkm.txt')) diff --git a/workflow/tests/test_inferMetadata.py b/workflow/tests/test_inferMetadata.py index 7485163631e2604ac2d5477a5c27b2fc9b235b44..1df1d296125f8a699e5c603eae8c9dfb61efd50c 100644 --- a/workflow/tests/test_inferMetadata.py +++ b/workflow/tests/test_inferMetadata.py @@ -12,4 +12,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.inferMetadata def test_inferMetadata(): assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_1M.se.inferMetadata.log')) + test_output_path, '16-WJRA_1M.se.inferMetadata.log')) diff --git a/workflow/tests/test_makeBigWig.py b/workflow/tests/test_makeBigWig.py index d8f62f5edfb3b57868d0b4b18ed6a0deb6bd651e..35492e886dc7c8c9c4ba2faaefd7c6cc6ae259ce 100644 --- a/workflow/tests/test_makeBigWig.py +++ b/workflow/tests/test_makeBigWig.py @@ -11,4 +11,4 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.makeBigWig def test_makeBigWig(): - assert os.path.exists(os.path.join(data_output_path, 'Q-Y5F6_1M.se.bw')) + assert os.path.exists(os.path.join(data_output_path, '16-WJRA_1M.se.bw')) diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py index f6373b99109e1d618dcb65559d24977140a125a4..431d9922d87a12d54890c3600a1cc1c5fceac0be 100644 --- a/workflow/tests/test_makeFeatureCounts.py +++ b/workflow/tests/test_makeFeatureCounts.py @@ -12,8 +12,8 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.makeFeatureCounts def test_makeFeatureCounts(): assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.countData')) + data_output_path, '16-WJRA_1M.se.countData')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se.countTable.csv')) + data_output_path, '16-WJRA_1M.se.countTable.csv')) assert os.path.exists(os.path.join( - data_output_path, 'Q-Y5F6_1M.se_tpmTable.csv')) + data_output_path, '16-WJRA_1M.se_tpmTable.csv')) diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py index a0938e756715fb30254e5c72fee4cd38bffec330..661663e0dfb21143ee48e933e0553503edb207e7 100644 --- a/workflow/tests/test_trimData.py +++ b/workflow/tests/test_trimData.py @@ -12,12 +12,12 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.trimData def test_trimData_se(): assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_1M.se_trimmed.fq.gz')) + test_output_path, '16-WJRA_1M.se_trimmed.fq.gz')) @pytest.mark.trimData def test_trimData_pe(): assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_1M.pe_val_1.fq.gz')) + test_output_path, '16-WJRA_1M.pe_val_1.fq.gz')) assert os.path.exists(os.path.join( - test_output_path, 'Q-Y5F6_1M.pe_val_2.fq.gz')) + test_output_path, '16-WJRA_1M.pe_val_2.fq.gz'))