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Freebayes: compress with bgzip (#1243)
* move to bgzip * update freebayes test results
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parent
080320765c
commit
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2 changed files with 22 additions and 7 deletions
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@ -41,7 +41,7 @@ process FREEBAYES {
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$args \\
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$input > ${prefix}.vcf
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gzip --no-name ${prefix}.vcf
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bgzip ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -60,7 +60,7 @@ process FREEBAYES {
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$args \\
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$input > ${prefix}.vcf
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gzip --no-name ${prefix}.vcf
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bgzip ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -1,34 +1,49 @@
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- name: freebayes test_freebayes
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command: nextflow run ./tests/modules/freebayes -entry test_freebayes -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
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command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
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tags:
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- freebayes
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: 81d3e6ce7b6343d088b779567c3803eb
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- path: output/freebayes/versions.yml
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md5sum: 53651eb835af65df829241257584a7d2
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- name: freebayes test_freebayes_bed
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command: nextflow run ./tests/modules/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
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command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
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tags:
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- freebayes
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: 02645d014a63485162a7789007373b2a
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- path: output/freebayes/versions.yml
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md5sum: becc93c8a0be580c09d55b955d60a5e1
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- name: freebayes test_freebayes_cram
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command: nextflow run ./tests/modules/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
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command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
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tags:
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- freebayes
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: 3d0bfcd2129c62f8863952fa4c1054db
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- path: output/freebayes/versions.yml
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md5sum: 2e5b266edfc6cab81353cfc72c00f67c
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- name: freebayes test_freebayes_somatic
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command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
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command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
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tags:
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- freebayes
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: 22fec868210ba3baf685b214bfd8e74b
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- path: output/freebayes/versions.yml
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md5sum: 8fbdb4c052fb3e42b5508a966125fa05
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- name: freebayes test_freebayes_somatic_cram_intervals
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command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
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command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
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tags:
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- freebayes
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: 527cf2937067bbd4117d95fd472bb928
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- path: output/freebayes/versions.yml
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md5sum: af97e3dfdc086188739907c3460e49e0
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