Describe the bug
It is not possible to run the output of a previous EAGER2 run, such as on the unmapped reads, again through the pipeline e.g.to a different reference.
The pipeline fails because it looks for the strings in the 'prefix' defined below, which if the sample has gone through the pipeline previously, will already have the string earlier in the file name. I presume this is because at the basename step it fails as it the program cannot find the erroneously truncated file name to the earlier generated prefix string.
i.e. SPYOLD_S0_L001_R1_001.fastq.merged.combined.sorted.bam.unmapped.combined
ERROR ~ Error executing process > 'bwa (SPYOLD_S0_L001_R1_001.fastq.merged.combined.sorted.bam.unmapped.combined)'
Caused by:
No such property: baseName for class: nextflow.util.BlankSeparatedList
Source block:
prefix = reads[0].toString() - ~/(_R1)?(\.combined\.)?(prefixed)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
fasta = "${index}/*.fasta"
"""
bwa aln -t ${task.cpus} $fasta $reads -n ${params.bwaalnn} -l ${params.bwaalnl} -k ${params.bwaalnk} -f "${reads.baseName}.sai"
bwa samse -r "@RG\\tID:ILLUMINA-${prefix}\\tSM:${prefix}\\tPL:illumina" $fasta "${reads.baseName}".sai $reads | samtools sort -@ ${task.cpus} -O bam - > "${prefix}".sorted.bam
samtools index "${prefix}".sorted.bam
"""
To Reproduce
Run a sample through the pipeline (v2.0.5) with the FASTQ having the duplicates of any of the prefix strings defined above (e.g. .combined.final.fastq.gz)
Describe the bug
It is not possible to run the output of a previous EAGER2 run, such as on the unmapped reads, again through the pipeline e.g.to a different reference.
The pipeline fails because it looks for the strings in the 'prefix' defined below, which if the sample has gone through the pipeline previously, will already have the string earlier in the file name. I presume this is because at the basename step it fails as it the program cannot find the erroneously truncated file name to the earlier generated prefix string.
i.e. SPYOLD_S0_L001_R1_001.fastq.merged.combined.sorted.bam.unmapped.combined
To Reproduce
Run a sample through the pipeline (
v2.0.5) with the FASTQ having the duplicates of any of the prefix strings defined above (e.g..combined.final.fastq.gz)