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NYU-Molecular-Pathology / NGS580-nf

Target exome sequencing analysis for NYU NGS580 gene panel
GNU General Public License v3.0
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filter for fastq with no reads #7

Closed stevekm closed 5 years ago

stevekm commented 5 years ago

Need to add some kind of channel filter or other sanity check to make sure that the fastq files have >0 reads in them. Had a case where I 'finalize''d the output then resumed the run and the empty fastq from 'fastq-merge' was used for the pipeline and immediately broke, need to prevent such situations

stevekm commented 5 years ago

Maybe better to just use the Makefile to leave a '.finalized' type of "lock" file to indicate that the run has been marked as "done" and then use this to trigger either a 'clean-all' or run without the -resume feature. This would be similar to the 'passed' feature of the demux-nf pipeline

stevekm commented 5 years ago

I think a better option is to re-configure the make finalize step to rename the file-stubs it leaves, so that Nextflow does not confuse them for the actual output files. For example, Sample1.fastq should become Sample1.fastq.stub

stevekm commented 5 years ago

not a real issue