BWA mem fails for paired-end sequencing data that shouldn't be collapsed due to wrong file suffix

[alexhbnr]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/eager pipeline documentation
  - nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

When aligning paired-end data that haven't been collapsed during adapter removal, bwa mem fails due to a missing file suffix. In line 1311 of main.nf, the output filename is "${libraryid}"_"${seqtype}".mapped.bam, however, samtools index in line 1312 is run on "${libraryid}".mapped.bam.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run ...
2. See error:

  [main] Version: 0.7.17-r1188
  [main] CMD: bwa mem -t 2.0 -R @RG\tID:ILLUMINA-MDC018_C0102_SG1\tSM:MDC018\tPL:illumina\tPU:ILLUMINA-MDC018_C0102_SG1-PE hs37d5/hs37d5.fa MDC018_C0102_SG1_R1_lanemerged.fq.gz MDC018_C0102_SG1_R2_lanemerged.fq.gz
  [main] Real time: 3388.526 sec; CPU: 6807.014 sec
  [bam_sort_core] merging from 14 files and 2 in-memory blocks...
  [E::hts_open_format] Failed to open file "MDC018_C0102_SG1.mapped.bam" : No such file or directory
  samtools index: failed to open "MDC018_C0102_SG1.mapped.bam": No such file or directory