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Freebayes: compress with bgzip (#1243)

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* move to bgzip
* update freebayes test results
This commit is contained in:
Maxime Borry 2022-01-31 10:11:39 +01:00 committed by GitHub
parent 080320765c
commit 7026122ec8
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 22 additions and 7 deletions
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4
modules/freebayes/main.nf
View file

@ -41,7 +41,7 @@ process FREEBAYES {
$args \\ $args \\
$input > ${prefix}.vcf $input > ${prefix}.vcf
gzip --no-name ${prefix}.vcf bgzip ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":
@ -60,7 +60,7 @@ process FREEBAYES {
$args \\ $args \\
$input > ${prefix}.vcf $input > ${prefix}.vcf
gzip --no-name ${prefix}.vcf bgzip ${prefix}.vcf
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

25
tests/modules/freebayes/test.yml
View file

@ -1,34 +1,49 @@
- name: freebayes test_freebayes - name: freebayes test_freebayes
command: nextflow run ./tests/modules/freebayes -entry test_freebayes -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
tags: tags:
- freebayes - freebayes
files: files:
- path: output/freebayes/test.vcf.gz - path: output/freebayes/test.vcf.gz
md5sum: 81d3e6ce7b6343d088b779567c3803eb
- path: output/freebayes/versions.yml
md5sum: 53651eb835af65df829241257584a7d2
- name: freebayes test_freebayes_bed - name: freebayes test_freebayes_bed
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
tags: tags:
- freebayes - freebayes
files: files:
- path: output/freebayes/test.vcf.gz - path: output/freebayes/test.vcf.gz
md5sum: 02645d014a63485162a7789007373b2a
- path: output/freebayes/versions.yml
md5sum: becc93c8a0be580c09d55b955d60a5e1
- name: freebayes test_freebayes_cram - name: freebayes test_freebayes_cram
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
tags: tags:
- freebayes - freebayes
files: files:
- path: output/freebayes/test.vcf.gz - path: output/freebayes/test.vcf.gz
md5sum: 3d0bfcd2129c62f8863952fa4c1054db
- path: output/freebayes/versions.yml
md5sum: 2e5b266edfc6cab81353cfc72c00f67c
- name: freebayes test_freebayes_somatic - name: freebayes test_freebayes_somatic
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
tags: tags:
- freebayes - freebayes
files: files:
- path: output/freebayes/test.vcf.gz - path: output/freebayes/test.vcf.gz
md5sum: 22fec868210ba3baf685b214bfd8e74b
- path: output/freebayes/versions.yml
md5sum: 8fbdb4c052fb3e42b5508a966125fa05
- name: freebayes test_freebayes_somatic_cram_intervals - name: freebayes test_freebayes_somatic_cram_intervals
command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
tags: tags:
- freebayes - freebayes
files: files:
- path: output/freebayes/test.vcf.gz - path: output/freebayes/test.vcf.gz
md5sum: 527cf2937067bbd4117d95fd472bb928
- path: output/freebayes/versions.yml
md5sum: af97e3dfdc086188739907c3460e49e0