Missing output file(s) `*_R1_primers-pass.fastq` about airrflow

[ggabernet]

Hi @LiuH2020 ,
thanks for trying out the pipeline. If you've used the full pipeline tests, it should work and I think this should be a transient error maybe. You also provided the Vprimers and Cprimers that are provided in the test_full.config, correct ? Have you tried resuming the run by running again the same command in the same directory but providing the extra option -resume ?

Otherwise I would just have the suggestion as well to run the pipeline directly from GitHub providing the version number with the parameter -r. As there will be the release 3.2.0 really soon, I would also suggest trying the dev version of the pipeline:

nextflow run nf-core/airrflow -r dev -profile docker,test_full --outdir result --max_memory 56.GB --max_cpus 4

Hope this works for you, let me know if you have any remaining errors that we can fix before the next release

[LiuH2020]

Thanks for your reply. According to your suggestions, I checked the Vprimers and Cprimers files. And found the used Vprimers and Cprimers is not right (download from the the airrflow branches of nf-core/test-datasets). The pipeline is OK when replacing them with downloaded from s3://ngi-igenomes/test-data/airrflow/pcr_umi/vprimers.fasta and s3://ngi-igenomes/test-data/airrflow/pcr_umi/cprimers.fasta.

For the Vprimers and Cprimers file, I have some questions: (1)The Vprimers and Cprimers files of airrflow branches of nf-core/test-datasets of nf-core/test-datasets) is fake? Not use them? (2) The Vprimers and Cprimers files of aws is real primers constructed based on sequences? (3) For some public dataset, if the primers they use cannot accessible, could these Vprimers and Cprimers of pipeline be used? or, needn't to input these primers file?

[ggabernet]

Great you could solve the issue with using the right primers!
The primers in the test-datasets repository are for small test data, which uses another dataset.
The primers really depend on the protocol that was used for sequencing, e.g. if the amplification of BCR / TCR was done with multiplexed PCRs or 5' RACE amplification. Maybe they describe whether they used a commercial kit for amplification?

I will close this issue meanwhile as the problem was solved, but feel free to continue asking questions regarding the primers. We also have a Slack channel on the nf-core slack for this kind of discussions: https://nf-co.re/join