neoflow
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bzhanglab
NeoFlow: a proteogenomics pipeline for neoantigen discovery
Hi, I got an error with calculateFDR in step2  Looking forward to your reply! Thank you very much!
I tried to use neoflow by exampledata.But I get an error when I run neoflow_msms.nf this is my code ` ./nextflow run ./neoflow-master/neoflow_msms.nf \ --ms /mnt/g/example_data/mgf \ --msms_para_file /mnt/g/example_data/comet_parameter.txt \...
I succeeded in running the STEP1, but **failed in STEP2**, all information I know about error are as follows : ``` Error executing process > 'msms_searching (spec-00139.mgf)' Caused by: Process...
I copied test data from example_data folder provided by the neoflow. the input_vcf_list.txt file looks like: ``` experiment sample file file_type crc_test sample1 /neoantigen2/input/sample1.vcf somatic ``` the copied sample1.vcf looks...
Hello, I tested all four modules with the example data, however, only module 1 and 3 finished successfully. I got the same error as issue #4 in module 2. As...
noeflow_db.nf doesn't allow the `-t` flag of `customProDBJ` which allows not having reference protein sequences being output. I did a quick fix here and am happy to open a PR....
I have been trying the 2. Variant peptide identification step with my own data and I keep getting the error that bioconductor is not updated which I already have along...
N E X T F L O W ~ version 19.10.0 Launching `neoflow_db.nf` [kickass_mcnulty] - revision: 96dbe17e38 Format input mapping file: /cbio/users/javanokendo/proteogenomics/example_data/test_vcf_files.tsv! New mapping file: ./test_vcf_files.tsv! executor > local (1)...
I am using neoflow and I am getting the following error with the example data that the pipeline comes with. What could be the problem? I am running this work...