From 9afa2ee97d25fb581c3efd50520ec4db3aa8def7 Mon Sep 17 00:00:00 2001 From: s181706 <jonathan.gesell@utsouthwestern.edu> Date: Fri, 24 Jan 2020 12:27:14 -0600 Subject: [PATCH] Corrected CI file. --- .gitlab-ci.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 7335a82..e108ad1 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -45,14 +45,14 @@ trimData: alignReads: stage: unit script: - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA.unal.gz -S Q-Y5JA.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 Q-Y5JA_R1_val_1.fq.gz -2 Q-Y5JA_R2_val_2.fq.gz 1>Q-Y5JA.align.out 2>Q-Y5JA.align.err - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA.bam Q-Y5JA.sam 1>>Q-Y5JA.align.out 2>>Q-Y5JA.align.err - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA.sorted.bam Q-Y5JA.bam 1>>Q-Y5JA.align.out 2>>Q-Y5JA.align.err - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA.sorted.bam Q-Y5JA.sorted.bai 1>>Q-Y5JA.align.out 2>>Q-Y5JA.align.err - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz 16-1ZX4.unal.gz -S 16-1ZX4.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U 16-1ZX4_trimmed.fq.gz 1>16-1ZX4.align.out 2>16-1ZX4.align.err - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o 16-1ZX4.bam 16-1ZX4.sam 1>>16-1ZX4.align.out 2>>16-1ZX4.align.err - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o 16-1ZX4.sorted.bam 16-1ZX4.bam 1>>16-1ZX4.align.out 2>>16-1ZX4.align.err - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b 16-1ZX4.sorted.bam 16-1ZX4.sorted.bai 1>>16-1ZX4.align.out 2>>16-1ZX4.align.err + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz ./test_data/fastq/Q-Y5JA.unal.gz -S ./test_data/fastq/Q-Y5JA.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/Q-Y5JA_R1_val_1.fq.gz -2 ./test_data/fastq/Q-Y5JA_R2_val_2.fq.gz + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ./test_data/fastq/Q-Y5JA.bam ./test_data/fastq/Q-Y5JA.sam + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o ./test_data/fastq/Q-Y5JA.sorted.bam ./test_data/fastq/Q-Y5JA.bam + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b ./test_data/fastq/Q-Y5JA.sorted.bam ./test_data/fastq/Q-Y5JA.sorted.bai + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz ./test_data/fastq/16-1ZX4.unal.gz -S ./test_data/fastq/16-1ZX4.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR -U ./test_data/fastq/16-1ZX4_trimmed.fq.gz + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o ./test_data/fastq/16-1ZX4.bam ./test_data/fastq/16-1ZX4.sam + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o ./test_data/fastq/16-1ZX4.sorted.bam ./test_data/fastq/16-1ZX4.bam + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b ./test_data/fastq/16-1ZX4.sorted.bam ./test_data/fastq/16-1ZX4.sorted.bai - pytest -m alignReads integration_se: -- GitLab