A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I’m not sure that <https://github.com/nf-core/bamtofastq/pull/149|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 <https://github.com/nf-core/bamtofastq/blob/8a295860c0c9221337dec7f2620709a47cea254d/conf/test.config#L26|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?

I just tried to run

```nextflow run main.nf -profile singularity --outdir out --input ../test_bam_samplesheet.csv```
on the branch `fix-test-profile` from PR#149, and it crashes with the expected error, that is,

```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> [...]]
...```

Yes I mean the current setup is that you have to supply either the genome or the fasta and that is not well explained (I just saw). Whether it makes sense that the fasta / genome is needed is another question. Maybe you can open an issue that says that we should evaluate when the fasta is needed and when its not needed and adapt the code accordingly.

I think the assumption was that people would always supply the `--genome` but thats not even stated in the README.

I think I can add to the quick fix this info and then we can have another PR that takes care of evaluating the fasta usage.

I don’t think specifying `--genome GRCh38` works in either v2.2.0 or v2.2.1 - at least it didn’t for me. That is, the igenomes-functionality doesn’t seem to work.

oh yeah that makes sense ...
can you open an issue please? Then I can tackle this when I find the time

I have continued on the PR, and now `nextflow run . -profile test,docker --outdir results` works without issues

all tests are :white_check_mark: : <https://github.com/nf-core/bamtofastq/pull/149>