command_id=53d5004a-f736-43cc-b3fc-3e009c038aaf
DAY-EC activated.
DAY-EC activated.
__DATE__=2026-06-03T03:45:15+00:00
wrote config/samples.tsv with 41 samples
wrote config/bclconvert_l003_scratch.yaml

__REPO_STATUS__
 M config/day/day_env_installer.sh
 M config/day_profiles/local/templates/rule_config.yaml
 M config/day_profiles/slurm/templates/rule_config.yaml
 M tests/test_bclconvert_bootstrap.sh
 M tests/test_bclconvert_multiqc.py
 M tests/test_shell_wrapper_contracts.py
 M workflow/rules/bclconvert.smk
 M workflow/scripts/run_bclconvert_lane.sh
?? config/bclconvert_l003_scratch.yaml

__CONFIG__
bootstrap_bclconvert: true
bclconvert:
  run_id: fasts_from_bclconvert_l003_scratch_test
  run_dir: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4
  sample_sheet: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/SampleSheet.csv
  output_root: /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4
  partition: bcl2fq
  constraint: ""
  threads: 48
  mem_mb: 300000
  tmpdir: /scratch/dayoa_bclconvert_tmp
  scratch_output_root: /scratch/dayoa_bclconvert
  parallel_tiles: 8
  conversion_threads: 2
  compression_threads: 24
  decompression_threads: 8
  tile_shard_level: lane
  tile_shard_lanes: "3"
  tile_shard_threads: 48
  tile_shard_mem_mb: 300000
  tile_parallel_tiles: 8
  tile_conversion_threads: 2
  tile_compression_threads: 24
  tile_decompression_threads: 8
  merge_lane_fastqs: false
  merge_tile_fastqs: false
  shared_thread_odirect_output: false
  fastq_gzip_compression_level: 1
  output_legacy_stats: true
  num_unknown_barcodes_reported: 1000
  strict_mode: false
  first_tile_only: false
  sampleproject_subdirectories: false
  keep_undetermined_fastqs: true

__SAMPLES__
42 config/samples.tsv
SAMPLEID	SAMPLESOURCE	SAMPLECLASS	BIOLOGICAL_SEX	CONCORDANCE_CONTROL_PATH	IS_POSITIVE_CONTROL	IS_NEGATIVE_CONTROL	SAMPLE_TYPE	TUM_NRM_SAMPLEID_MATCH	EXTERNAL_SAMPLE_ID	N_X	N_Y	TRUTH_DATA_DIR
HG001-a	blood	research	unknown	na	false	false	blood	na	HG001-a	na	na	na
HG001-b	blood	research	unknown	na	false	false	blood	na	HG001-b	na	na	na
HG001-c	blood	research	unknown	na	false	false	blood	na	HG001-c	na	na	na
HG002-a	blood	research	unknown	na	false	false	blood	na	HG002-a	na	na	na

__DEST__
drwxr-xr-x 2 ubuntu ubuntu 33792 Jun  3 03:43 /fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/fasts_from_bclconvert_l003_scratch_test
dest_file_count=0

__CONTRACT_PROBES__
config/day_profiles/slurm/templates/rule_config.yaml:132:    scratch_output_root: ""
config/day_profiles/slurm/templates/rule_config.yaml:138:    tile_shard_lanes: ""
workflow/scripts/run_bclconvert_lane.sh:30:scratch_output_root="${27:-}"
workflow/scripts/run_bclconvert_lane.sh:48:if [[ -n "$scratch_output_root" ]]; then
workflow/scripts/run_bclconvert_lane.sh:49:  if [[ "$scratch_output_root" != /* ]]; then
workflow/scripts/run_bclconvert_lane.sh:50:    echo "bclconvert.scratch_output_root must be an absolute path: $scratch_output_root" >> "$log_path"
workflow/scripts/run_bclconvert_lane.sh:54:  scratch_work_dir="${scratch_output_root%/}/dayoa_bclconvert_${SLURM_JOB_ID:-manual_$$}/${safe_output_id}"
workflow/scripts/run_bclconvert_lane.sh:77:echo "scratch_output_root: ${scratch_output_root:-<none>}" >> "$log_path"
workflow/scripts/run_bclconvert_lane.sh:93:if [[ -n "$scratch_output_root" ]]; then
workflow/scripts/run_bclconvert_lane.sh:94:  singularity_bind_args+=(--bind "$scratch_output_root:$scratch_output_root")
workflow/rules/bclconvert.smk:151:BCL_CONSTRAINT = str(BCLCFG.get("constraint", "") or "")
workflow/rules/bclconvert.smk:153:BCL_SCRATCH_OUTPUT_ROOT = str(BCLCFG.get("scratch_output_root", "") or "").rstrip("/")
workflow/rules/bclconvert.smk:263:BCL_TILE_SHARD_LANES_RAW = BCLCFG.get("tile_shard_lanes", "")
workflow/rules/bclconvert.smk:311:        raise WorkflowError("bclconvert.tile_shard_lanes includes absent lanes: " + ",".join(unknown))
workflow/rules/bclconvert.smk:517:        constraint=BCL_CONSTRAINT,
workflow/rules/bclconvert.smk:528:        scratch_output_root=BCL_SCRATCH_OUTPUT_ROOT,
workflow/rules/bclconvert.smk:560:        "{output.demux_stats:q} {output.done:q} \"\" {params.scratch_output_root:q}"
workflow/rules/bclconvert.smk:579:        constraint=BCL_CONSTRAINT,
workflow/rules/bclconvert.smk:589:        scratch_output_root=BCL_SCRATCH_OUTPUT_ROOT,
workflow/rules/bclconvert.smk:622:        "{output.demux_stats:q} {output.done:q} {params.tile_regex:q} {params.scratch_output_root:q}"
workflow/rules/bclconvert.smk:654:        constraint=BCL_CONSTRAINT,
workflow/rules/bclconvert.smk:704:            constraint=BCL_CONSTRAINT,
workflow/rules/bclconvert.smk:744:            constraint=BCL_CONSTRAINT,
workflow/rules/bclconvert.smk:902:        constraint=BCL_CONSTRAINT,
