Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update ALL bcftools modules #3339

Merged
merged 2 commits into from
Apr 26, 2023
Merged

Update ALL bcftools modules #3339

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
bfa6272
CHORES: update ALL bcftools modules
maxulysse Apr 26, 2023
1753038
update md5sum
maxulysse Apr 26, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/call/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_CALL {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(index)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/concat/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcfs), path(tbi)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/consensus/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(tbi), path(fasta)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/convert/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_CONVERT {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(input), path(input_index)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/filter/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/index/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
tag "$meta.id"
label 'process_low'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/isec/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcfs), path(tbis)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/merge/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcfs), path(tbis)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/mpileup/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_MPILEUP {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(bam), path(intervals)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/norm/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(tbi)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/query/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(tbi)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/reheader/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
tag "$meta.id"
label 'process_low'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(header)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/roh/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_ROH {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(tbi)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/sort/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_SORT {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/split/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_SPLIT {
tag "$meta.id"
label 'process_single'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(tbi)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/stats/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
tag "$meta.id"
label 'process_single'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(tbi)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/bcftools/view/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
tag "$meta.id"
label 'process_medium'

conda "bioconda::bcftools=1.16"
conda "bioconda::bcftools=1.17"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bcftools:1.16--hfe4b78e_1':
'quay.io/biocontainers/bcftools:1.16--hfe4b78e_1' }"
'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
'quay.io/biocontainers/bcftools:1.17--haef29d1_0' }"

input:
tuple val(meta), path(vcf), path(index)
Expand Down
20 changes: 10 additions & 10 deletions tests/modules/nf-core/bcftools/mpileup/test.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,11 @@
- bcftools
files:
- path: output/bcftools/test.bcftools_stats.txt
md5sum: 0a6fb5b79930bb2c3c179619380e8ebf
md5sum: 652ead9184c18167613a3bfc75b99111
- path: output/bcftools/test.vcf.gz.tbi
md5sum: 2198b362ec46027623f2cc5da5881777
md5sum: 23e5a910227891c53bb34196be7c00b4
- path: output/bcftools/test.vcf.gz
md5sum: f0e3b1b665205909b52226473b5bf8fb
md5sum: 960b84036dd0a532b338b1a95813fc25

- name: bcftools mpileup test_bcftools_save_mpileup
command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config
Expand All @@ -18,13 +18,13 @@
- bcftools
files:
- path: output/bcftools/test.bcftools_stats.txt
md5sum: 0a6fb5b79930bb2c3c179619380e8ebf
md5sum: 652ead9184c18167613a3bfc75b99111
- path: output/bcftools/test.vcf.gz.tbi
md5sum: 2198b362ec46027623f2cc5da5881777
md5sum: 23e5a910227891c53bb34196be7c00b4
- path: output/bcftools/test.vcf.gz
md5sum: f0e3b1b665205909b52226473b5bf8fb
md5sum: 960b84036dd0a532b338b1a95813fc25
- path: output/bcftools/test.mpileup.gz
md5sum: 175e7e6edf0ca24bf6cfffe5a3bf7061
md5sum: dd424be36720bb09007233bd367796f1

- name: bcftools mpileup test_bcftools_mpileup_intervals
command: nextflow run ./tests/modules/nf-core/bcftools/mpileup -entry test_bcftools_mpileup_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/mpileup/nextflow.config
Expand All @@ -33,8 +33,8 @@
- bcftools
files:
- path: output/bcftools/test.bcftools_stats.txt
md5sum: d91d947ec3822ecabf28d474babc303c
md5sum: 405eee1f452446e34f3dcfc2b00e5fab
- path: output/bcftools/test.vcf.gz.tbi
md5sum: d655c592ab8ef5c834cdd19dc1022fec
md5sum: 3a50baca0fb70eaab68c44cb9bd4d4a3
- path: output/bcftools/test.vcf.gz
md5sum: d0e1b95b45610fe37bee5712a9bb0124
md5sum: 1feaf4810f6b57f32ea7fd2dbc4da9a0
1 change: 0 additions & 1 deletion tests/subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/test.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@
contains:
- "chr22\t1982\t.\tA\tG\t459.724"
- path: output/bcftools/aligned.sorted.vcf.gz.csi
md5sum: 93ecb3ee8fb165cbd754e1a1676e41fe
- path: output/freebayes/aligned.vcf.gz
contains:
- "chr22\t1982\t.\tA\tG\t459.724"