A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

:x: *sarek/test_full_germline_aws* failed :crying_cat_face: *Run Name*
irreverent_lichterman *Duration*
4h 18m 13s *Status*
:x: Failed *Error Message*
```(more omitted..)
I1110 01:24:05.758458 140476293185984 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I1110 01:24:05.758535 140386039812544 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I1110 01:24:05.773899 139923034407360 make_examples_core.py:3855] model.example_info filename: /opt/models/wgs/model.example_info.json
I1110 01:24:05.774254 139923034407360 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wgs/model.example_info.json
I1110 01:24:05.774579 139923034407360 make_examples_core.py:3876] Flags for calling:
call_small_model_examples: True
pileup_image_height: 100
pileup_image_width: 221
small_model_indel_gq_threshold: 28
small_model_snp_gq_threshold: 20
small_model_vaf_context_window_size: 51
track_ref_reads: True
trained_small_model_path: /opt/smallmodels/wgs/model.keras
W1110 01:24:05.774679 139923034407360 make_examples_core.py:3890] Flag call_small_model_examples is specified in model.example_info.json [True] but overridden by command line with value [True]
I1110 01:24:05.777362 139923034407360 dv_utils.py:333] From /opt/models/wgs/model.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1110 01:24:05.777558 139923034407360 make_examples_options.py:1233] Parsing AUX Fields: []
W1110 01:24:05.777813 139923034407360 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1110 01:24:05.779291 139923034407360 make_examples_core.py:384] Task 3/12: Preparing inputs
I1110 01:24:05.821645 139923034407360 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I1110 01:24:06.589347 139840407241152 make_examples_core.py:384] Task 0/12: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'c...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name irreverent_lichterman -params-file '<https://api.cloud.seqera.io/ephemeral/bDAWOMgDfxZTfRY1I2OWZg.json>' -with-tower -r dev -profile test_full_germline_aws``` Nov 10, 2026 at 1:24 AM