Closed
Description
Description of the bug
The ID field should have ${flowcell}.${row.sample}.${row.lane}
flowcell gets resolved to null, so I'm guessing something with the flowcellLaneFromFastq() function.
cf AWS megatests in tower:
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
bwa mem \
-K 100000000 -Y -R "@RG\tID:null.HCC1395N.1\tPU:1\tSM:HCC1395_HCC1395N\tLB:HCC1395N\tDS:s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta\tPL:ILLUMINA" \
-t 16 \
$INDEX \
0001.HCC1395N-1_1.fastp.fastq.gz 0001.HCC1395N-1_2.fastp.fastq.gz \
| samtools sort --threads 16 -o HCC1395N-1.0001.bam -
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP:BWAMEM1_MEM":
bwa: $(echo $(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*$//')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS
Command used and terminal output
No response
Relevant files
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System information
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