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Require PacBio CLR data to be bam files #28

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j23414 opened this issue Nov 17, 2021 · 1 comment
Open

Require PacBio CLR data to be bam files #28

j23414 opened this issue Nov 17, 2021 · 1 comment

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@j23414
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j23414 commented Nov 17, 2021

If PacBio data is passed in as a fasta file, the @RG annotation is lost, and Arrow gccp will complain

gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short

Maybe can check for .fasta or fa extension and print a warning. Or hack an acceptable @RG annotation...

@j23414
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j23414 commented Dec 22, 2022

Could add guard-rails here to throw an error if the user passes in a fasta file instead of the required bam file:

polishCLR/main.nf

Lines 227 to 236 in d1a1b9f

if(params.pacbio_reads){
pacbio_reads_ch = channel.fromPath(params.pacbio_reads, checkIfExists:true)
| view {file -> "PacBio Reads: $file"}
pacbio_all_ch = pacbio_reads_ch
| collect
| map {n -> [n]}
} else {
exit 1, "[Missing File(s) Error] polishCLR requires '--pacbio_reads [PacBio bam file]' for ArrowPolish steps.\n"
}

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