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:
Describe the bug
When running with the
-singularityprofile on the branches/versions-r shh-profileand-r 2.0.2, thebwamodule crashes on thesamtools indexon the sorted bamfile.It appears there maybe a misplaced
-@option which is not applicable tosamtools index.Samtools standard out/error is below:
To Reproduce
Run the following command (replace paired end data, index file as required):
Additional context
Please provide me with the following files:
.nextflow.lognextflow.logresults/pipeline_info/...pipeline_report.txt