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Bwa index (#1040)

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* fix a bug that the prefix is not handled by index.

* build the test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
JIANHONG OU 2021-11-15 06:26:01 -05:00 committed by GitHub
parent 94851901d5
commit 9475960928
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2 changed files with 12 additions and 12 deletions
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4
modules/bwa/index/main.nf
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@ -31,8 +31,8 @@ process BWA_INDEX {
bwa \\
index \\
$options.args \\
$fasta \\
-p bwa/${fasta.baseName}
-p bwa/${fasta.baseName} \\
$fasta
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:

20
tests/modules/bwa/index/test.yml
View file

@ -1,16 +1,16 @@
- name: bwa index
command: nextflow run ./tests/modules/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
- name: bwa index test_bwa_index
command: nextflow run tests/modules/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
tags:
- bwa
- bwa/index
files:
- path: ./output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: ./output/bwa/bwa/genome.amb
- path: output/bwa/bwa/genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1
- path: ./output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwa/bwa/genome.ann
- path: output/bwa/bwa/genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567
- path: output/bwa/bwa/genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: output/bwa/bwa/genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: output/bwa/bwa/genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1