admin
12/15/2025, 3:56 AMnextflow 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 \
-resumeChannel Helper - help
12/15/2025, 6:38 AM... 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 @Phil Ewels for help.Channel Helper - help
12/15/2025, 6:40 AM... 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.