IsoSeq Clustering (Refine + Cluster)
Clustering: C57 K1-50pM (individual)
Type
CWL
Status
succeeded
Engine
cwltool
Duration
0.2 h
Source Data
Pipeline
PacBio CCS (Subreads → HiFi)
IsoSeq Clustering (Refine + Cluster)
Run #81
(this run)
succeeded
1 sources
IsoSeq Annotation (Map + Collapse + SQANTI3)
Functional Annotation (TransDecoder + Pfam + SwissProt)
Combined From
- #76 — PacBio CCS (Subreads → HiFi) succeeded
Workflow
IsoSeq Clustering (Refine + Cluster)
#cwl
Software Tools
| Tool | Version | URL |
|---|---|---|
| cwltool | - | https://github.com/common-workflow-language/cwltool |
Results Summary
Input CCS Reads
139,403
FLNC Reads
136,489
Mean FLNC Length
0 nt
HQ Isoforms
0
LQ Isoforms
0
Clustering Ratio
0.0
FLNC / HQ isoforms
Mean FL Support
6.6
reads per isoform
Total FL Reads
91,987
Output Files
Provenance
| Execution | Expression quantification summary |
| Completed | 2026-03-04T12:44:10+00:00 |
RO-Crate 1.1
Workflow RO-Crate 1.0
FAIR
This analysis is packaged as a Research Object Crate
with machine-readable provenance and FAIR metadata.
RO-Crate Metadata (JSON-LD)
Show/hide raw JSON-LD
{
"@context": "https://w3id.org/ro/crate/1.1/context",
"@graph": [
{
"@id": "ro-crate-metadata.json",
"@type": "CreativeWork",
"about": {
"@id": "./"
},
"conformsTo": [
{
"@id": "https://w3id.org/ro/crate/1.1"
},
{
"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
}
]
},
{
"@id": "./",
"@type": "Dataset",
"name": "IsoSeq Clustering (Refine + Cluster) \u2014 Run #81",
"description": "Generic IsoSeq3 clustering pipeline. Merges demultiplexed BAMs, runs primer removal + polyA filtering (refine), then clusters into HQ/LQ isoform consensus sequences. Compatible with Sequel I CCS (use_qvs=false) and Sequel II/IIe HiFi data.",
"datePublished": "2026-03-04",
"license": {
"@id": "https://creativecommons.org/licenses/by/4.0/"
},
"mainEntity": {
"@id": "isoseq_clustering.cwl"
},
"hasPart": [
{
"@id": "isoseq_clustering.cwl"
},
{
"@id": "job.yml"
},
{
"@id": "clustered.hq.bam"
},
{
"@id": "clustered.lq.bam"
},
{
"@id": "clustered.cluster_report.csv"
},
{
"@id": "clustered.cluster"
},
{
"@id": "flnc.filter_summary.report.json"
},
{
"@id": "flnc.bam"
},
{
"@id": "clustered.hq.bam.pbi"
},
{
"@id": "demux_primers.lima.summary"
},
{
"@id": "flnc.bam.pbi"
},
{
"@id": "clustered.lq.bam.pbi"
},
{
"@id": "results_summary.json"
},
{
"@id": "summary_extractor.py"
}
],
"mentions": [
{
"@id": "#execution"
},
{
"@id": "#summary-extraction"
}
]
},
{
"@id": "isoseq_clustering.cwl",
"@type": [
"File",
"SoftwareSourceCode",
"ComputationalWorkflow"
],
"name": "IsoSeq Clustering (Refine + Cluster)",
"description": "#cwl",
"programmingLanguage": {
"@id": "Generic IsoSeq3 clustering pipeline. Merges demultiplexed BAMs, runs primer removal + polyA filtering (refine), then clusters into HQ/LQ isoform consensus sequences. Compatible with Sequel I CCS (use_qvs=false) and Sequel II/IIe HiFi data."
},
"contentSize": "2.9 KB",
"sha256": "3cd8cfcc8caaf0fb4a964a16fc02edffbddb048e0c46b8c633c8fd3abf7efa08"
},
{
"@id": "#cwl",
"@type": "ComputerLanguage",
"name": "Common Workflow Language",
"url": {
"@id": "https://www.commonwl.org/"
},
"version": "1.2"
},
{
"@id": "#cwltool",
"@type": "SoftwareApplication",
"name": "cwltool",
"url": {
"@id": "https://github.com/common-workflow-language/cwltool"
}
},
{
"@id": "job.yml",
"@type": "File",
"name": "job.yml",
"description": "CWL job input parameters",
"encodingFormat": "text/yaml",
"contentSize": "278 B",
"sha256": "3540d952c99745823a5ca9c99afa8bfed9ab0dd0cd11c4645b98d18e08a6eee1"
},
{
"@id": "clustered.hq.bam",
"@type": "File",
"name": "clustered.hq.bam",
"encodingFormat": "application/octet-stream",
"contentSize": "11.7 MB",
"sha256": "61ab93f801ae27449487614a30e44bbad9069354bc8f9785fb8121967b516e4b"
},
{
"@id": "clustered.lq.bam",
"@type": "File",
"name": "clustered.lq.bam",
"encodingFormat": "application/octet-stream",
"contentSize": "3.2 KB",
"sha256": "19532569d412792f29a313e8b637be479137820600776bbddb4a0d11ba155530"
},
{
"@id": "clustered.cluster_report.csv",
"@type": "File",
"name": "clustered.cluster_report.csv",
"encodingFormat": "text/csv",
"contentSize": "4.7 MB",
"sha256": "9396d55f689dd51f470905455f533c355c7d9da8c54a1931eeebaeecf976603f"
},
{
"@id": "clustered.cluster",
"@type": "File",
"name": "clustered.cluster",
"encodingFormat": "application/octet-stream",
"contentSize": "6 MB",
"sha256": "2be2e179192336f0ec8181acbdeecbe5dec0752ee04b6a5ae53bfe2bd30aa5b0"
},
{
"@id": "flnc.filter_summary.report.json",
"@type": "File",
"name": "flnc.filter_summary.report.json",
"encodingFormat": "application/json",
"contentSize": "819 B",
"sha256": "359fa32673fcaf99546875f69c63953afcf553e0b797d5f261ab75b6e2f81f1c"
},
{
"@id": "flnc.bam",
"@type": "File",
"name": "flnc.bam",
"encodingFormat": "application/octet-stream",
"contentSize": "320 MB",
"sha256": "68e433638cc341627de25b20b2d0ed31abb80c6a71f2a9841b253ef39295a73c"
},
{
"@id": "clustered.hq.bam.pbi",
"@type": "File",
"name": "clustered.hq.bam.pbi",
"encodingFormat": "application/octet-stream",
"contentSize": "80.2 KB",
"sha256": "9827a82c50f9bc4720e170ff15a0857123a829d06a9f276fa6e87ce147bdf7e2"
},
{
"@id": "demux_primers.lima.summary",
"@type": "File",
"name": "demux_primers.lima.summary",
"encodingFormat": "application/octet-stream",
"contentSize": "917 B",
"sha256": "9dd0fdadf6a72d9ccc6f3f752c314dbc7d29f40ba77ae04c10f2bb17e265990f"
},
{
"@id": "flnc.bam.pbi",
"@type": "File",
"name": "flnc.bam.pbi",
"encodingFormat": "application/octet-stream",
"contentSize": "1.4 MB",
"sha256": "f94cd3354d2aa668ea0ee0fa48a626b3777b8403f8ccec6bd53565cb3401e18d"
},
{
"@id": "clustered.lq.bam.pbi",
"@type": "File",
"name": "clustered.lq.bam.pbi",
"encodingFormat": "application/octet-stream",
"contentSize": "101 B",
"sha256": "e22c627e5eee1b83c2e989699a67c78a7b1ffc3331c184001ba2cfcc0b3c8540"
},
{
"@id": "#execution",
"@type": "CreateAction",
"name": "IsoSeq Clustering (Refine + Cluster) execution",
"instrument": {
"@id": "isoseq_clustering.cwl"
},
"startTime": "2026-03-04T22:32:17+00:00",
"endTime": "2026-03-04T12:43:56+00:00",
"object": [
{
"@id": "job.yml"
}
],
"result": [
{
"@id": "clustered.hq.bam"
},
{
"@id": "clustered.lq.bam"
},
{
"@id": "clustered.cluster_report.csv"
},
{
"@id": "clustered.cluster"
},
{
"@id": "flnc.filter_summary.report.json"
},
{
"@id": "flnc.bam"
},
{
"@id": "clustered.hq.bam.pbi"
},
{
"@id": "demux_primers.lima.summary"
},
{
"@id": "flnc.bam.pbi"
},
{
"@id": "clustered.lq.bam.pbi"
}
]
},
{
"@id": "results_summary.json",
"@type": "File",
"name": "results_summary.json",
"description": "Derived summary statistics from pipeline outputs (CPM >= 1, uniquely mapped reads)",
"encodingFormat": "application/json",
"contentSize": "276 B",
"sha256": "d0a0c230102c51d61d4b17bc8d5a3e86b9441c63e1397130d82e60a351dee246"
},
{
"@id": "summary_extractor.py",
"@type": [
"File",
"SoftwareSourceCode"
],
"name": "Summary extraction script",
"description": "Python script that computed results_summary.json from pipeline outputs",
"programmingLanguage": {
"@id": "#python3"
}
},
{
"@id": "#python3",
"@type": "ComputerLanguage",
"name": "Python",
"url": {
"@id": "https://www.python.org/"
},
"version": "3"
},
{
"@id": "#summary-extraction",
"@type": "CreateAction",
"name": "Expression quantification summary",
"instrument": {
"@id": "summary_extractor.py"
},
"endTime": "2026-03-04T12:44:10+00:00",
"object": [
{
"@id": "OUT.read_assignments.tsv.gz"
},
{
"@id": "OUT.gene_counts.tsv"
},
{
"@id": "OUT.transcript_counts.tsv"
},
{
"@id": "OUT.extended_annotation.gtf"
},
{
"@id": "OUT.transcript_models.gtf"
}
],
"result": [
{
"@id": "results_summary.json"
}
]
}
]
}