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Allow BAM as input for long-reads submission

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@Vkale1 已经在做这个了。

开始于 2026年10月15日。

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难度
5/5
预计耗时
一周以上
新手友好度
42/100
Issue 类型
功能
描述清晰度
基本清楚
活跃度
活跃
领域
data-engineering

调研方向

首先定位 raw-read 文件类型处理以及基因组上传步骤的 Nextflow 参数。检查现有的 genome_uploader PR，并确认 PacBio 和 ONT 格式的 ENA 提交要求。完成的标准是：单 contig 长读长基因组和 FastQ/BAM 提交能够端到端运行，并且在大型上传后能够正常重试。

由索引模型根据 Issue 内容生成。

描述

enhancement

Description of feature

1. Long-read raw read submission (--mode reads)

Samplesheet schema (assets/schema_input_reads.json)

  • fastq_1 only accepts FASTQ. Add a new bam column, and require either fastq_1 or bam. A separate column is clearer than widening the fastq_1 pattern, since ENA treats BAM as its own manifest field.
  • Only allow bam when platform is OXFORD_NANOPORE or PACBIO_SMRT, and require fastq_2 to be empty for those platforms.
  • To confirm: leave out .tar.gz until ENA confirms whether it will still be supported.
    Workflow (workflows/readsubmit.nf)
  • Update the samplesheet mapping for the new bam column and record the file type (FASTQ or BAM) in meta.
    Manifest creation (modules/local/create_reads_manifest/main.nf)
  • Add BAM support so the manifest gets a BAM line instead of FASTQ lines.
  • To confirm: whether create_reads_manifest in mgnify-pipelines-toolkit (1.5.1) supports BAM.

2. Make BAM uploads retry cleanly

  • ENA_WEBIN_CLI_WRAPPER only retries on a few exit codes, once. Network failures during upload usually aren't retried. Add a withName block in conf/modules.config that retries on any failure, at least 3 times, with more time per attempt.
  • If an upload succeeds but the task fails afterwards, the retry will be rejected by ENA as already submitted. Check that the wrapper treats this as success and recovers the accession; if not, fix upstream.
  • The wrapper copies input files into the work directory. Switch to symlinks if Webin-CLI allows it, to save disk and time.
  • Optional: expose Webin-CLI's Aspera option for faster uploads (needs Aspera in the container).

3. Raw read tests

  • Add a small ONT FASTQ and a small long-read BAM to nf-core/test-datasets.
  • Add tests test_reads_long_fastq and test_reads_long_bam.
主要语言
Nextflow
星标
22
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11
平均合并
1 天 4 小时
30 天内合并 PR
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