From 3dff84f8eddc887f4811c347c94233b59ac9aacd Mon Sep 17 00:00:00 2001 From: Jonathan Gesell <jonathan.gesell@utsouthwestern.edu> Date: Wed, 12 Feb 2020 14:07:00 -0600 Subject: [PATCH] Update .gitlab-ci.yml --- .gitlab-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a4c2f3e..5ed5cc5 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -51,11 +51,11 @@ trimData: alignData: stage: unit script: - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.se.unal.gz -S Q-Y5JA_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.se.bam Q-Y5JA_1M.se.sam - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.bam - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.se.sorted.bam Q-Y5JA_1M.se.sorted.bai - - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz + - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p `nproc` --add-chrname --un-gz Q-Y5JA_1M.pe.unal.gz -S Q-Y5JA_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/Q-Y5JA_1M_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5JA_1M_R2_val_2.fq.gz - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ `nproc` -F 4 -F 8 -F 256 -o Q-Y5JA_1M.pe.bam Q-Y5JA_1M.pe.sam - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.bam - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b Q-Y5JA_1M.pe.sorted.bam Q-Y5JA_1M.pe.sorted.bai -- GitLab