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Mpileup intervals (#1955)

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* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* include intervals

* update md5 with interval

Co-authored-by: Smith Nicholas <smith@in.tum.de>
This commit is contained in:
nickhsmith 2022-08-16 14:16:35 +02:00 committed by GitHub
parent 458f4396a6
commit 454e0acc09
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2 changed files with 2 additions and 1 deletions
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1
modules/samtools/mpileup/main.nf
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@ -26,6 +26,7 @@ process SAMTOOLS_MPILEUP {
--fasta-ref $fasta \\ --fasta-ref $fasta \\
--output ${prefix}.mpileup \\ --output ${prefix}.mpileup \\
$args \\ $args \\
$intervals \\
$input $input
bgzip ${prefix}.mpileup bgzip ${prefix}.mpileup
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

2
tests/modules/samtools/mpileup/test.yml
View file

@ -15,5 +15,5 @@
- samtools/mpileup - samtools/mpileup
files: files:
- path: output/samtools/test.mpileup.gz - path: output/samtools/test.mpileup.gz
md5sum: 29455c36377196e8bc9cf831cf17b5dc md5sum: d0538ec23b294245748ced92484b9a8d
- path: output/samtools/versions.yml - path: output/samtools/versions.yml