带奇点的Snakemake

Question

我正在尝试在我的Snakemake规则中使用奇点。当在本地运行我的Snakemake流水线时，这是预期的。然而，当我尝试使用sbatch提交到我的计算集群时，我遇到了错误。我想知道您是否有任何建议，关于如何将本地管道转换为可以在集群上工作的管道。提前谢谢你！

导致错误的规则使用奇点来调用带有DeepVariant的变量：

# Call variants with DeepVariant.
rule deepvariant_call:
  input:
    ref_path='/labs/jandr/walter/varcal/data/refs/{ref}.fa',
    bam='results/{samp}/bams/{samp}_{mapper}_{ref}.rmdup.bam'
  params:
    nshards='1',
    version='0.7.0'
  threads: 8
  output:
    vcf='results/{samp}/vars/{samp}_{mapper}_{ref}_deep.g.vcf.gz'
  shell:
    'singularity exec --bind /srv/gsfs0 --bind /labs/jandr/walter/ /home/kwalter/.singularity/shub/deepvariant-docker-deepvariant:0.7.0.simg \
    /labs/jandr/walter/tb/test/scripts/call_deepvariant.sh {input.ref_path} {input.bam} {params.nshards} {params.version} {output.vcf} '
#
# Error in rule deepvariant_call:
#     jobid: 17
#     output: results/T1-XX-2017-1068_S51/vars/T1-XX-2017-1068_S51_bowtie2_H37Rv_deep.g.vcf.gz
#     shell:
#         singularity exec --bind /srv/gsfs0 --bind /labs/jandr/walter/ /home/kwalter/.singularity/shub/deepvariant-docker-deepvariant:0.7.0.simg;     /labs/jandr/walter/tb/test/scripts/call_deepvariant.sh /labs/jandr/walter/varcal/data/refs/H37Rv.fa results/T1-XX-2017-1068_S51/bams/T1-XX-2017-1068_S51_bowtie2_H37Rv.rmdup.bam 1 0.7.0 results/T1-XX-2017-1068_S51/vars/T1-XX-2017-1068_S51_bowtie2_H37Rv_deep.g.vcf.gz 
#         (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

我使用以下内容向集群提交作业：

snakemake -j 128 --cluster-config cluster.json --cluster "sbatch -A {cluster.account} --mem={cluster.mem} -t {cluster.time} -c {threads}"

Answer 1

从error message的resolved命令中可以看到，该错误是由shell:中的字符串格式引起的，该命令用分号分隔两行shell:，而不是空格。

您可以使用三引号格式：

  shell:
    '''
    singularity exec --bind /srv/gsfs0 --bind /labs/jandr/walter/ /home/kwalter/.singularity/shub/deepvariant-docker-deepvariant:0.7.0.simg \
    /labs/jandr/walter/tb/test/scripts/call_deepvariant.sh {input.ref_path} {input.bam} {params.nshards} {params.version} {output.vcf} 
    '''

或者，单引号中的每一行：

  shell:
    'singularity exec --bind /srv/gsfs0 --bind /labs/jandr/walter/ /home/kwalter/.singularity/shub/deepvariant-docker-deepvariant:0.7.0.simg \'
    '/labs/jandr/walter/tb/test/scripts/call_deepvariant.sh {input.ref_path} {input.bam} {params.nshards} {params.version} {output.vcf}'