OK, so merged the template, we are fine in terms of GHA or nf-schema, but a bit lacking behind in terms of modules update. How about we update modules, do nf-test for all tests and do a release?

@Maxime Garcia Not sure yet, but I will get back to you

Can we enable squash & merge for this pipeline aswell? :)

We want to add everyone who contributed to this pipeline to the nextflow.config file 🙂

[
            name: 'Famke Bäuerle',
            affiliation: 'Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany',
            email: '<mailto:famke.baeuerle@uni-tuebingen.de|famke.baeuerle@uni-tuebingen.de>',
            github: '@famosab',
            contribution: ['contributor'],
            orcid: '0000-0003-1387-0251'
        ],

Please either give me that info or edit the file in this PR (or post a comment in the PR): https://github.com/nf-core/bamtofastq/pull/114/files

First batch of module updates: https://github.com/nf-core/bamtofastq/pull/115

More updates: https://github.com/nf-core/bamtofastq/pull/116

<!here> Please check the contributors file here: https://github.com/nf-core/bamtofastq/pull/114/files If you want to submit more info or do not want to be listed please make a comment on the PR. I just added everyone that wwas listed by github. I want to close the PR next Monday 🙂

Something with the pattern check for fasta_fai was not working so I removed the whole check, but I am happy to adjust this to a regex that works: https://github.com/nf-core/bamtofastq/pull/118 (I had a look at the schema in sarek and there also no pattern is given :D)

I tried coming up with an addition that solves issue 70 (check for truncated files). Its not the most elegant way at the moment: Maybe also the module I used needs to be implemented differently. https://github.com/nf-core/bamtofastq/pull/120 I would try to finalize this and then go for a release afterwards

Any reason why we use samtools fastq instead of https://bedtools.readthedocs.io/en/latest/content/tools/bamtofastq.html for single end reads?

@Famke Bäuerle Do you want regular meetings to check-up and figure out what needs to be done before the release?

Hello <!channel>, we were wondering what was the actual usage of this pipeline. Do you use single ended 1️⃣ or pair ended 2️⃣ reads or both 👿 ?

Both 😈

I went a head and did a prepare release PR: https://github.com/nf-core/bamtofastq/pull/123 because the milestone is full party parrot maybe we can get this merged and then search for reviewers for the release?

What is the issue with the full size tests?

one process is taking WAAAY too long and dies out

so 6+ hours for something that should take less than 10 sec

Here is one run that completed: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/2FhAY2PJew6LtH/v2/tasks with aws-nofusion-test-ireland and one after that one that did not https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3Szj2hwYx9DL6P/v2/logs with aws_ireland_fusionv2_nvme_cpu - how should we continue? Is there a way to specifyy the compute environment, so that it works when I do the release again?

Hi all, I am running nf-core/bamtofastq to convert CRAM files into FASTQ files. What happens with the unmapped reads that were preserved in the CRAM file? What happens with the unmapped reads during the conversion to FASTQ? Can I save the unmapped_1.fq and unmapped_2.fq as output? [vsc46248@gligar10 DNA141207]$ samtools flagstat DNA141207.cram 94606758 + 0 in total (QC-passed reads + QC-failed reads) 94606758 + 0 primary 0 + 0 secondary 0 + 0 supplementary 8566647 + 0 duplicates 8566647 + 0 primary duplicates 93816793 + 0 mapped (99.16% : N/A) 93816793 + 0 primary mapped (99.16% : N/A) 94606758 + 0 paired in sequencing 47303379 + 0 read1 47303379 + 0 read2 92647620 + 0 properly paired (97.93% : N/A) 93544458 + 0 with itself and mate mapped 272335 + 0 singletons (0.29% : N/A) 803486 + 0 with mate mapped to a different chr 589777 + 0 with mate mapped to a different chr (mapQ>=5) [vsc46248@gligar10 DNA141207]$ samtools view -c -f 4 DNA141207.cram 789965 #C050TCYSCFM

✅ bamtofastq/test_full completed successfully! 🎉 Run Name berserk_davinci Duration 52m 48s Status ✅ Success Tasks Completed: 16 May 7, 2026 at 12:30 PM 🔗 View in Seqera Platform button

I am finalizing the next release and I am a bit unsure whether we should go for 2.2.1 or 2.3.0 - it contains mainly code maintenance, template updates, strict syntax and so on, updates to a few modules but no new feature in that sense. See https://github.com/nf-core/bamtofastq/pull/140 - let me know your thoughts.

New release is out 🎉 https://github.com/nf-core/bamtofastq/releases/tag/2.2.1 The pipeline is now compatible with strict syntax and has the latest module versions!

✅ bamtofastq/test_full completed successfully! 🎉 Run Name jovial_booth Duration 43m 58s Status ✅ Success Tasks Completed: 16 May 13, 2026 at 12:01 PM 🔗 View in Seqera Platform button

✅ bamtofastq/test_full completed successfully! 🎉 Run Name infallible_gutenberg Duration 10h 44m Status ✅ Success Tasks Completed: 16, Failed: 1 May 13, 2026 at 9:15 PM 🔗 View in Seqera Platform button

Hi guys. The test-profile of bamtofastq v2.2.1 doesn’t seem to work. I run

nextflow run nf-core/bamtofastq -profile test,singularity --outdir out

and it fails with

ERROR ~ Error executing process > 'NFCORE_BAMTOFASTQ:BAMTOFASTQ:PREPARE_INDICES:SAMTOOLS_FAIDX ([])'

Caused by:
  Process `NFCORE_BAMTOFASTQ:BAMTOFASTQ:PREPARE_INDICES:SAMTOOLS_FAIDX ([])` terminated with an error exit status (1)


Command executed:

  samtools \
      faidx \
       \


  cut -f 1,2 .fai > .sizes

Command exit status:
  1

Command output:
  Usage: samtools faidx <file.fa|file.fa.gz> [<reg> [...]]
  Option:
    -o, --output FILE        Write FASTA to file.
    -n, --length INT         Length of FASTA sequence line. [60]
    -c, --continue           Continue after trying to retrieve missing
...

Also, I don’t see any test results for v2.2.1 here: https://nf-co.re/bamtofastq/releases_stats/

I wonder why there is only the NCBI-GRCH38 fasta in the igenomes.config for bamtofastq and not also the GATK-GRCh38 like in sarek. 🤔

I’m not sure that PR#149 actually fixes the problem in the pipeline, although it does probably make the test-profile run. I would expect bamtofastq to be able to run with the following command

nextflow run nf-core/bamtofastq -r 2.2.1 -profile singularity --outdir out --input test_bam_samplesheet.csv

where

test_bam_samplesheet.csv

is just my local copy of the input csv-file from the test.config. However, it fails on v2.2.1. Is a command like that able to run after the fix in PR#149?

✅ bamtofastq/test_full completed successfully! 🎉 Run Name spontaneous_edison Duration 41m 39s Status ✅ Success Tasks Completed: 16 Jul 24, 2026 at 2:13 PM