Possibly faulty samtools index command?

[jfy133]

Describe the bug
When running with the -singularity profile on the branches/versions -r shh-profile and -r 2.0.2, the bwa module crashes on the samtools index on the sorted bamfile.

It appears there maybe a misplaced -@ option which is not applicable to samtools index.

Samtools standard out/error is below:

[main] CMD: bwa samse -r @RG\tID:ILLUMINA-ABM006.A0101_S0_L002_R1_001\tSM:ABM006.A0101_S0_L002_R1_001\tPL:illumina hg19_MT.fasta ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.sai ABM006.A0101_S0_L002_R1_001.combined.prefixed.fq.gz
  [main] Real time: 7.227 sec; CPU: 6.184 sec
  index: invalid option -- '@'
  Usage: samtools index [-bc] [-m INT] <in.bam> [out.index]
  Options:
    -b       Generate BAI-format index for BAM files [default]
    -c       Generate CSI-format index for BAM files
    -m INT   Set minimum interval size for CSI indices to 2^INT [14]

To Reproduce
Run the following command (replace paired end data, index file as required):

nextflow run nf-core/eager \
--reads '/projects1/users/fellows/nextflow/eager2/my_test/data/ABM006.A0101/*_R{1,2}*fastq.gz' \
--pairedEnd \
--fasta '/projects1/users/fellows/nextflow/eager2/my_test/references/hg19_MT.fasta' \
--outdir '/projects1/users/fellows/nextflow/eager2/my_test/output_eager2' \
-profile singularity \
--max_cpus 4 \
--max_memory 16G \
-r 2.0.2

Additional context
Please provide me with the following files:

• .nextflow.log nextflow.log
• results/pipeline_info/... pipeline_report.txt

[apeltzer]

I'm quite wondering why this wasn't caught by our CI tests at all. Samtools in the container should actually work fine and the -@ option was present...

[jfy133]

Odd... is the reference already indexed in the test?

Will test at the weekend once the fix is in the wild.

[apeltzer]

No, it isn't - just downloading FastA there. Though this error happens on the BAM level, creating indices for BAM files using samtools index <input.bam>

[apeltzer]

So my tests were correctly done - I guess indexing doesn't really benefit from parallelization anyways ;-)