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Hi, I am trying to run the oncoanalyser 2.1.0 for ...
# oncoanalyser
l
Hi, I am trying to run the oncoanalyser 2.1.0 for my tumor only WGS bam files. I am using this command Also, the params file.
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nextflow run nf-core/oncoanalyser \
 -profile docker \
 -r 2.1.0 \
 --mode wgts \
 --genome GRCh38_hmf \
 --input /home/isilon/patho_anemone-meso/fastq/dedup/samtools/Samplesheet.csv \
 --outdir results/ \
 -work-dir work/ \
 --processes_manual \
 --processes_include isofox,redux,amber,cobalt,purple,linx,sage,pave,esvee,lilac,cuppa \
 --redux_umi \
 --redux_umi_duplex_delim "-" \
 -c params.config \
 --resume

params file:
process {
    withName: '.*ALIGN'        { cpus = 12; memory = 72.GB; }
    withName: AMBER            { cpus = 16; memory = 24.GB; }
    withName: BAMTOOLS         { cpus = 16; memory = 24.GB; }
    withName: CHORD            { cpus = 4;  memory = 12.GB; }
    withName: COBALT           { cpus = 16; memory = 24.GB; }
    withName: CUPPA            { cpus = 4;  memory = 16.GB; }
    withName: 'ESVEE.*'        { cpus = 16; memory = 64.GB; }
    withName: LILAC            { cpus = 16; memory = 24.GB; }
    withName: 'LINX.*'         { cpus = 16; memory = 16.GB; }
    withName: REDUX            { cpus = 16; memory = 64.GB; }
    withName: ORANGE           { cpus = 4;  memory = 16.GB; }
    withName: 'PAVE.*'         { cpus = 8;  memory = 32.GB; }
    withName: PURPLE           { cpus = 8;  memory = 40.GB; }
    withName: 'SAGE.*'         { cpus = 16; memory = 64.GB; }
    withName: VIRUSBREAKEND    { cpus = 8;  memory = 64.GB; }
    withName: VIRUSINTERPRETER { cpus = 2;  memory = 8.GB;  }
}

process {
    resourceLimits = [
        cpus:   16,
        memory: 124.GB,
        disk:   1500.GB,
        time:   48.h
    ]
}
process {
    executor = "slurm"
}

params {
    // FASTQ UMI processing
    fastp_umi = true
    fastp_umi_location = "per_read"
    fastp_umi_length = 7
    fastp_umi_skip = 0

    // BAM UMI processing
    redux_umi = true
    redux_umi_duplex_delim = "-"

}
But I'm getting this error. I would appreciate any help.
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N E X T F L O W  ~ version 25.04.6
Launching `<https://github.com/nf-core/oncoanalyser>` [nostalgic_ritchie] DSL2 - revision: 0d0dc258ce [2.1.0]

ERROR ~ Cannot invoke method toUpperCase() on null object

 -- Check script '/home/gpfs/o_lipika/.nextflow/assets/nf-core/oncoanalyser/workflows/targeted.nf' at line: 13 or see '.nextflow.log' file for more details
r
Hi Lipika, could you share you .nextflow.log ?
l
Please find it attached.
nextflow (2).log
r
could you remove the umi and redux-related argument in your the cli command and try again ?
l
Copy code
nextflow run nf-core/oncoanalyser \
  -profile docker \
  -r 2.1.0 \
  --mode wgts \
  --genome GRCh38_hmf \
  --input /home/isilon/patho_anemone-meso/fastq/dedup/samtools/Samplesheet.csv \
  --outdir results/ \
  -work-dir work/ \
  --processes_manual \
  --processes_include isofox,redux,amber,cobalt,purple,linx,sage,pave,esvee,lilac,cuppa \
  -c params.config \
  --resume

 N E X T F L O W   ~  version 25.04.6

Launching `<https://github.com/nf-core/oncoanalyser>` [infallible_panini] DSL2 - revision: 0d0dc258ce [2.1.0]

ERROR ~ Cannot invoke method toUpperCase() on null object

 -- Check script '/home/gpfs/o_lipika/.nextflow/assets/nf-core/oncoanalyser/workflows/targeted.nf' at line: 13 or see '.nextflow.log' file for more details
Also the nextflow.log file
nextflow (1).log
r
could you try this instead of work-dir ? 
workDir =
it also can be defined in your config
l
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nextflow run nf-core/oncoanalyser \
  -profile docker \
  -r 2.1.0 \
  --mode wgts \
  --genome GRCh38_hmf \
  --input /home/isilon/patho_anemone-meso/fastq/dedup/samtools/Samplesheet.csv \
  --outdir results/ \
  --workDir work/ \
  --processes_manual \
  --processes_include isofox,redux,amber,cobalt,purple,linx,sage,pave,esvee,lilac,cuppa \
  -c params.config \
  --resume

 N E X T F L O W   ~  version 25.04.6

Launching `<https://github.com/nf-core/oncoanalyser>` [fervent_ramanujan] DSL2 - revision: 0d0dc258ce [2.1.0]

ERROR ~ Cannot invoke method toUpperCase() on null object

 -- Check script '/home/gpfs/o_lipika/.nextflow/assets/nf-core/oncoanalyser/workflows/targeted.nf' at line: 13 or see '.nextflow.log' file for more details
nextflow (2).log
r
Could you share your samplesheet ? something's not parsing on that end I think
l
Samplesheet (1).csv
Samplesheet (1).csv
r
the column should be comma-separated - could you try that ?
l
So nice, it worked. Thankyou. I have two more question, as in the oncoanalyser pipeline, it is suggested to run redux even on bams which are already deduplicated. I have bams which are deduplicated using samtools markdup (v1.21). What will be the pros and cons of not using redux? Last, is there any difference if I use the hmftools directly using jars and without oncoanalyser? Thank you in advance :)
r
no problem, we've designed redux to maximize the types of sequencing platforms that can make use of oncoanalyser and prepare the input optimally for the rest of the tools in the workflow. REDUX is therefore recommended. Not using it will make it harder to debug whether an issue lies in the file contents themselves or elsewhere. There should be no differences between running w/ the jar themselves or oncoanalyser but it will make the task much more complicated given the complexity of the tools and how intertwined they all are. Oncoanalyser guarantees that the right output is fed into the pertinent next step, so on and so forth. I'd therefore advise to use that, simply for convenience. I hope that answers your questions! 🙂
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