I run my WES data with sarek option '--step mappin...
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a
I run my WES data with sarek option '--step mapping', but the script ends before variant_calling process without any errors.It doesn't match what was written in the doc, anything wrong implements with me?bash commands are as follows
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nextflow run nf-core/sarek \
    -profile docker \
    -c nextflow.config \
    --input "${INPUT_CSV}" \
    --outdir "${OUTDIR}" \
    --max_cpus 9 \
    --max_memory '45.GB' \
    --wes \
    --step mapping \
    --intervals "${REF_DIR}/exome_capture_kit_fixed.bed" \
    --genome GATK.GRCh38 \
    --tools mutect2,lofreq,strelka,manta,tiddit,cnvkit,controlfreec,msisensor2,snpeff,vep,indexcov \
    --trim_fastq \
    -with-report "${OUTDIR}/pipeline_info/execution_report.html" \
    -with-trace "${OUTDIR}/pipeline_info/execution_trace.txt" \
    -with-timeline "${OUTDIR}/pipeline_info/execution_timeline.html" \
    -with-dag "${OUTDIR}/pipeline_info/pipeline_dag.html" \
    --save_mapped \
    --save_output_as_bam \
    -resume
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c
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Hi, @admin! Slack uses channels to organise discussions. Press the
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more
option on the left sidebar. Then hover over Your organisation, and finally select Channels to browse. Each nf-core pipeline has it’s own channel (e.g. #CE8SSJV3N). Please post any questions about specific pipelines in the relevant channel. If you’re not sure where to post your message, please ask @admin for help.