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Add_minleghth_0_fasterq_dump #220

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Add_minleghth_0_fasterq_dump #220

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robsyme
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@robsyme robsyme commented Oct 14, 2023

Previously, if the sample contains empty reads, they would be quietly
discarded:

$ fastq-dump --split-files SRR12848126
Rejected 52 READS because READLEN < 1
Read 1517 spots for SRR12848126
Written 1517 spots for SRR12848126

This can cause problems when using paired end reads in downstream
processes that expect len(R1) == len(R2).

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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e8ef56a

+| ✅ 148 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: lib/WorkflowFetchngs.groovy
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-14 19:31:59

@robsyme
Download all reads by default to ensure paired ends have equal reads.
e8ef56a 
Previously, if the sample contains empty reads, they would be quietly
discarded:

```
$ fastq-dump --split-files SRR12848126
Rejected 52 READS because READLEN < 1
Read 1517 spots for SRR12848126
Written 1517 spots for SRR12848126
```

This can cause problems when using paired end reads in downstream
processes that expect len(R1) == len(R2).

Signed-off-by: Rob Syme <rob.syme@gmail.com>
@robsyme robsyme force-pushed the add_minleghth_0_fasterq_dump branch from 3904d4f to e8ef56a Compare October 14, 2023 19:30
@robsyme
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robsyme commented Oct 14, 2023

Actually, this doesn't yet fix the problem. Using fastq-dump works:

$ fastq-dump --split-files --minReadLen 0 SRR12848126; wc -l *.fastq
Read 1517 spots for SRR12848126
Written 1517 spots for SRR12848126
     6068 SRR12848126_1.fastq
     6068 SRR12848126_2.fastq
    12136 total

But fasterq-dump refuses to return equal-length fastq files:

$ fasterq-dump --split-files --min-read-len 0 SRR12848126; wc -l *.fastq
spots read      : 1,517
reads read      : 3,034
reads written   : 2,982
     5940 SRR12848126_1.fastq
     5988 SRR12848126_2.fastq
    11928 total

Closing this PR until I can work out how to force fasterq-dump to return matched fastq files.

@robsyme robsyme closed this Oct 14, 2023
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