Hi,
Firstly, I made a docker version of dkfzbiasfilter, version 1.2.3. However, when I run it with the following command, got an error saying OSError: [Errno 2] No such file or directory: '/var/spool/cwl/filtered_qcSummary'
docker run -v /abosulute_path/test_res/test.sorted.rmdup.realigned.recal.bam -v /abosulute_path/test_res/test.sorted.rmdup.realigned.recal.bam.bai -v /abosulute_path/test_res/hg19.fa -v /abosulute_path/test_res/test.vcf -v /abosulute_path/test_res/test_res dkfzbiasfilter:1.2.3
Secondly, I also installed your conda version of code. But I was not able to find the filtered_vcf_file.
Third, is it a must to use the hs37d5.fa?
Thank you very much!
Best,
Yu
Hi,
Firstly, I made a docker version of dkfzbiasfilter, version 1.2.3. However, when I run it with the following command, got an error saying OSError: [Errno 2] No such file or directory: '/var/spool/cwl/filtered_qcSummary'
docker run -v /abosulute_path/test_res/test.sorted.rmdup.realigned.recal.bam -v /abosulute_path/test_res/test.sorted.rmdup.realigned.recal.bam.bai -v /abosulute_path/test_res/hg19.fa -v /abosulute_path/test_res/test.vcf -v /abosulute_path/test_res/test_res dkfzbiasfilter:1.2.3
Secondly, I also installed your conda version of code. But I was not able to find the filtered_vcf_file.
Third, is it a must to use the hs37d5.fa?
Thank you very much!
Best,
Yu