diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c31b9dc941934dbc26716739ca211976365a9ade..6ea53a7f0dc2a8265a0a93ba8cfd4ef0dd9afc1b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -53,7 +53,7 @@ alignReads: - 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 - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ `nproc` -O BAM -o 16-1ZX4.sorted.bam 16-1ZX4.bam - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b 16-1ZX4.sorted.bam 16-1ZX4.sorted.bai - - pytest -m alignReads + - pytest -m alignData integration_se: stage: integration