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Revert PR #1147 (#1166)

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* Revert PR #1147

* Fix md5sum for crai file
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Harshil Patel 2021-12-13 16:15:20 +00:00 committed by GitHub
parent 47a9cf8ecb
commit 0fafaeebf5
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2 changed files with 5 additions and 8 deletions
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5
modules/samtools/index/main.nf
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@ -11,12 +11,9 @@ process SAMTOOLS_INDEX {
tuple val(meta), path(input) tuple val(meta), path(input)
output: output:
tuple val(meta), path("*.bam" , includeInputs:true), path("*.bai") , optional:true, emit: bam_bai
tuple val(meta), path("*.bai") , optional:true, emit: bai tuple val(meta), path("*.bai") , optional:true, emit: bai
tuple val(meta), path("*.bam" , includeInputs:true), path("*.csi") , optional:true, emit: bam_csi
tuple val(meta), path("*.csi") , optional:true, emit: csi tuple val(meta), path("*.csi") , optional:true, emit: csi
tuple val(meta), path("*.cram", includeInputs:true), path("*.crai"), optional:true, emit: cram_crai tuple val(meta), path("*.crai"), optional:true, emit: crai
tuple val(meta), path("*.crai") , optional:true, emit: crai
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
script: script:

2
tests/modules/samtools/index/test.yml
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@ -14,7 +14,7 @@
- samtools/index - samtools/index
files: files:
- path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai - path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
md5sum: 537e3d8c937bcc4e34e1cf47cd71d484 md5sum: 14bc3bd5c89cacc8f4541f9062429029
- name: samtools index test_samtools_index_csi - name: samtools index test_samtools_index_csi
command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config command: nextflow run ./tests/modules/samtools/index -entry test_samtools_index_csi -c ./tests/config/nextflow.config -c ./tests/modules/samtools/index/nextflow.config