Closed LilyAnderssonLee closed 3 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit ac04c4a
+| ✅ 266 tests passed |+
!| ❗ 2 tests had warnings |!
@jfy133The log file of Porechop_ABI
is almost same as the one from Porechop
. I am wondering if we could use the MultiQC/porechop
module to process Porechop_ABI
log files. If so, could you please add that to the multiqc.yml
file? I am not very familiar with that.
multiqc_report_porechop: multiqc_report_porechop.html.zip multiqc_report_porechop_abi: multiqc_report_porechop_abi.html.zip
I had a look a tthe MultiuQC reports - they look good except the file/sample names are dfiferent, the ABI is missing the library/run ID (just sample ID)... do you know why that is?
Yah I found the issue. Multiqc/porechop
takes the sample name from the fastq.gz
file at the beginning of the log file.
Top rows of porechop_abi
log file:
[1m[4mLoading reads[0m
ERR3201952.fastq.gz
10,000 reads loaded
Top rows of porechop
log file:
[1m[4mLoading reads[0m
ERR3201952_ERR3201952_porechop.fastq.gz
10,000 reads loaded
No wait, I think this fastq.gz
file passed from the upstream. I will check the source of the file.
Yeah, the problem is spotted. The porechop
module was modified by adding a line to create a soft link to ensure the ID matches the rest of the pipeline based on meta.id
rather than the input file name. I did the same for the porechop_abi
Porechop_abi multiqc report: multiqc_report_new.html.zip
OK! Then one last thing, in the multiqc_config yaml unde 'extra_fn_clean_exts:' can you add 'postchop_abi` or whatever the suffix is? That way MultiQC will clean the sample name for us for rendering :)
Updated. Not sure why linting
failed here, but passed locally.
extra_fn_clean_exts:
- "kraken2.report.txt"
- ".txt"
- ".settings"
- ".bbduk"
- ".unmapped"
- "_filtered"
- "porechop.log"
- "porechop_abi.log"
- type: remove
pattern: "_falco"
Can yuou send a MultiQC report of with each tool as a final check?
@jfy133 Can we merge this PR now?
Thank you very much @LilyAnderssonLee !
Add
Porechop_ABI
to the pipeline as an alternative for adapter removal in long-read Oxford Nanopore data.Close the issue https://github.com/nf-core/taxprofiler/issues/145
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).