DAY-EC activated.
DAY-EC activated.
=== bclconvert rule patch ===
341:                scratch_run_dir="$scratch_dir/run"
343:                mkdir -p "$scratch_run_dir"
359:                cp -aL --sparse=always "$effective_run_dir"/. "$scratch_run_dir"/
360:                effective_run_dir="$scratch_run_dir"
367:                scratch_run_dir="$scratch_dir/run"
372:                mkdir -p "$scratch_run_dir" "$scratch_sync_log_dir"
412:                mkdir -p "$scratch_run_dir/Data/Intensities/BaseCalls"
416:                      | xargs -0 -r cp -L --sparse=always -t "$scratch_run_dir"
418:                      | xargs -0 -r cp -L --sparse=always -t "$scratch_run_dir/Data/Intensities"
445:                    scratch_run_dir="$2"
449:                        dst="$scratch_run_dir/Data/Intensities/BaseCalls/$(dirname "$rel")"
453:                ' _ "$lane_root" "$scratch_run_dir" \
461:                du -sh "$scratch_run_dir" >> {log:q} 2>&1 || true
462:                effective_run_dir="$scratch_run_dir"
469:                scratch_run_dir="$scratch_dir/run"
472:                mkdir -p "$scratch_run_dir" "$scratch_sync_log_dir"
517:                  aws s3 sync "$run_uri/" "$scratch_run_dir/" \
530:                          aws s3 sync "$run_uri/Data/Intensities/BaseCalls/$lane_id/" "$scratch_run_dir/Data/Intensities/BaseCalls/$lane_id/" \
547:                du -sh "$scratch_run_dir" >> {log:q} 2>&1 || true
548:                effective_run_dir="$scratch_run_dir"
606:            echo "Moving BCLConvert outputs from scratch to result tree: $(date -Is)" >> {log:q}
610:            if [ -n "${{scratch_run_dir:-}}" ] && [ -d "$scratch_run_dir" ]; then
611:                echo "Removing staged BCL input scratch: $scratch_run_dir $(date -Is)" >> {log:q}
612:                rm -rf "$scratch_run_dir"
=== active profile bclconvert block ===
path=config/day_profiles/local/templates/rule_config.yaml
bclconvert:
    run_dir: ""
    sample_sheet: "SampleSheet.csv"
    output_root: "results/bclconvert"
    run_id: ""
    libprep: "PCR-FREE"
    seq_vendor: "ILMN"
    seq_platform_override: ""
    force: false
    keep_undetermined_fastqs: true
    sampleproject_subdirectories: false
    strict_mode: false
    first_tile_only: false
    extra_args: ""
    threads: 7
    mem_mb: 16000
    partition: "i8"
    tmpdir: "/dev/shm"
    staging_mode: "direct"
    scratch_root: "/dev/shm/dayoa_bclconvert"
    scratch_size_multiplier: 4
    retain_scratch: false
    parallel_tiles: 1
    conversion_threads: 3
    compression_threads: 3
    decompression_threads: 1
    fastq_gzip_compression_level: 1
    shared_thread_odirect_output: false

