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VAriantcaller with multiple outputs causes MQC issues & interval names not resolved correctly for prefixes #567

Merged
merged 65 commits into from
Jun 8, 2022
Merged

VAriantcaller with multiple outputs causes MQC issues & interval names not resolved correctly for prefixes #567

merged 65 commits into from
Jun 8, 2022

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FriederikeHanssen
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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).

@FriederikeHanssen
remove manta from annotation with vep, svtype is not comaptible
1246bb5
@FriederikeHanssen
fix mix up of processes
a344fe0
@FriederikeHanssen
fix mix up of processes
ae1bd3c
@FriederikeHanssen
use new_intervals & fix which manta vcfs should get annotated
aa6617a
@FriederikeHanssen
missed on emeta map
e290a37
@FriederikeHanssen
remove leftover print statement
6292615
@FriederikeHanssen
fix channel mapping and execute CI test
21b7679
@FriederikeHanssen
why is interval naming with meta maps not working
a145363
@FriederikeHanssen
revert changes
605232a
@FriederikeHanssen
actually copy the interval file name each time
b6a4a8f
@FriederikeHanssen
also copy read map
e054fdc
@FriederikeHanssen
new String also doesn't work
abc92fc
@FriederikeHanssen
alright tired of this, try resolving prefix/interval name in the config
5f9e968
@FriederikeHanssen
exclude manta from annotation
cd6a922
@FriederikeHanssen
Use new name resolution for paired
6fe6019
@FriederikeHanssen
mpileup naming
1a3c8aa
@FriederikeHanssen
replace prefix in conf for all variantcalling
7dd54e4
@FriederikeHanssen
replace prefix for preprocessing
8a03b1d
@FriederikeHanssen
fix mutect f1r2 output name
59e4c6f
@FriederikeHanssen
multiqc multi files
8a520ec
@FriederikeHanssen
print out mqc file
aa9cf84
@FriederikeHanssen
no manta and veo
f3d5f1d
@FriederikeHanssen
manta and strelka have multiple vcf outputs
87de6cd
@FriederikeHanssen
split strelka vcf to avoid duplicate annotation filenames
cf12b92
@FriederikeHanssen
split strelka vcf to avoid duplicate annotation filenames
c77f452
@FriederikeHanssen
split strelka vcf to avoid duplicate annotation filenames
6a7d37f
@FriederikeHanssen
remove view
b2d9fa3
@FriederikeHanssen
add empty channel names
7c6d53d
@FriederikeHanssen
if starting from step annotation meta.vc is empty
1e194ee
@FriederikeHanssen
update test path
d1271e2
@maxulysse
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gatk4_spark is failing as usual.
strelka and haplotypecaller are failing.
nf-core linting is failing too, is that expected?
deepvariant and freebayes are taking their time

@FriederikeHanssen
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linting is failing because a while back I messed around in ascat. Susanne will fix it. Strelka should not fail. I'll restart to see if it is just a glitch

maxulysse
maxulysse reviewed Jun 3, 2022
View reviewed changes
conf/modules.config
@@ -1025,10 +1025,11 @@ process{
}

withName: ".*:ANNOTATION_MERGE:ENSEMBLVEP" {
ext.prefix = {"${meta.id}_snpEff"}
ext.prefix = { meta.variantcaller ? meta.type ? "${meta.variantcaller}_${meta.id}_${meta.type}_snpEff_VEP.ann.vcf" : "${meta.variantcaller}_${meta.id}_snpEff_VEP.ann.vcf" : "${meta.id}_snpEff_VEP.ann.vcf" }
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<3

maxulysse
maxulysse approved these changes Jun 3, 2022
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AMAZING

@maxulysse
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removed ascat from modules.json to get linting to pass

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github-actions bot commented Jun 3, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d18de9e

+| ✅ 144 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • schema_description - No description provided in schema for parameter: umi_read_structure
  • schema_description - No description provided in schema for parameter: group_by_umi_strategy

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-08 09:59:23

@maxulysse maxulysse merged commit 68687ef into nf-core:dev Jun 8, 2022
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@FriederikeHanssen @maxulysse