Fix intervals

[FriederikeHanssen]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nickhsmith]

do you know how it'll interact with the other modules that use num_intervals? In the variant calling subworkflow the input cram_recalibrated_intervals now contains the num_intervals. But modules such as:

subworkflows/nf-core/gatk4/prepare_recalibration/main.nf
subworkflows/nf-core/gatk4/prepare_recalibration_spark/main.nf
subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
subworkflows/nf-core/variantcalling/deepvariant/main.nf
subworkflows/nf-core/variantcalling/freebayes/main.nf
subworkflows/nf-core/variantcalling/haplotypecaller/main.nf
subworkflows/nf-core/variantcalling/manta/germline/main.nf
subworkflows/nf-core/variantcalling/manta/somatic/main.nf
subworkflows/nf-core/variantcalling/manta/tumoronly/main.nf
subworkflows/nf-core/variantcalling/strelka/single/main.nf
subworkflows/nf-core/variantcalling/strelka/somatic/main.nf

all group by num_intervals outside of the cram or input channel.

[FriederikeHanssen]

do you know how it'll interact with the other modules that use num_intervals? In the variant calling subworkflow the input cram_recalibrated_intervals now contains the num_intervals. But modules such as:

subworkflows/nf-core/gatk4/prepare_recalibration/main.nf
subworkflows/nf-core/gatk4/prepare_recalibration_spark/main.nf
subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
subworkflows/nf-core/variantcalling/deepvariant/main.nf
subworkflows/nf-core/variantcalling/freebayes/main.nf
subworkflows/nf-core/variantcalling/haplotypecaller/main.nf
subworkflows/nf-core/variantcalling/manta/germline/main.nf
subworkflows/nf-core/variantcalling/manta/somatic/main.nf
subworkflows/nf-core/variantcalling/manta/tumoronly/main.nf
subworkflows/nf-core/variantcalling/strelka/single/main.nf
subworkflows/nf-core/variantcalling/strelka/somatic/main.nf

all group by num_intervals outside of the cram or input channel.

Yeah they all need fixing. I have it done aprtially locally already but haven't had time to push the fixes yet. Also want to remove the querying for no_intervlas in the grouping as it should be unnecessary now

[maxulysse]

Issues with the new modules when merging?
I can see there is more local modules than I expected

[FriederikeHanssen]

Issues with the new modules when merging? I can see there is more local modules than I expected

🤦‍♀️ yep messed up merging.

[maxulysse]

Issues with the new modules when merging? I can see there is more local modules than I expected

woman_facepalming yep messed up merging.

😱

[FriederikeHanssen]

honestly not sure what happened, but oh well

[maxulysse]

num_intervals is 0 for params.no_intervals?
Shouldn't it be 1 as for just one big interval?

[FriederikeHanssen]

quite a philosophical question. I was thinking of num_intervals as num_interval_files.

This does avoid the whole weird things about querying for interval file name for the VC workflows:

            new_meta.id = num_intervals <= 1 ? meta.sample : meta.sample + "_" + intervals.baseName
            new_meta.num_intervals = num_intervals

            //If no interval file provided (0) then add empty list
            intervals_new = num_intervals == 0 ? [] : intervals
            ```

[FriederikeHanssen]

OK there are still both cosmetic problems:

1. interval names not matching (old "bug") file content is fine, it is just about the naming
2. saveAs creating empty files

[maxulysse]

Mutect2 for next PR?

[FriederikeHanssen]

Mutect2 for next PR?

Yes I think this is a separate issue topic wise + want to coordinate with @GCJMackenzie on this

[FriederikeHanssen]

OK there are still both cosmetic problems:

1. interval names not matching (old "bug") file content is fine, it is just about the naming

2. saveAs creating empty files

Follow up issue: #534

[maxulysse]

<3