Skip to content

Commit

Permalink
Move conda-checks (third batch) (nf-core#3692)
Browse files Browse the repository at this point in the history 
Moving conda-check and replacing exit 1 with error-cmd
  • Loading branch information
@asp8200
asp8200 authored Aug 3, 2023
1 parent 0caab70 commit b9172e8
Show file tree
Hide file tree
Showing 7 changed files with 32 additions and 35 deletions.
9 changes: 4 additions & 5 deletions modules/nf-core/sentieon/applyvarcal/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,6 @@ process SENTIEON_APPLYVARCAL {

secret 'SENTIEON_LICENSE_BASE64'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
}

container 'nf-core/sentieon:202112.06'

input:
Expand All @@ -26,6 +21,10 @@ process SENTIEON_APPLYVARCAL {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
Expand Down
13 changes: 8 additions & 5 deletions modules/nf-core/sentieon/bwaindex/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,6 @@ process SENTIEON_BWAINDEX {
label 'process_high'
label 'sentieon'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
}

container 'nf-core/sentieon:202112.06'

input:
Expand All @@ -21,6 +16,10 @@ process SENTIEON_BWAINDEX {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
"""
mkdir bwa
Expand All @@ -39,6 +38,10 @@ process SENTIEON_BWAINDEX {
"""

stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
"""
mkdir bwa
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/sentieon/bwamem/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,6 @@ process SENTIEON_BWAMEM {

secret 'SENTIEON_LICENSE_BASE64'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
}

container 'nf-core/sentieon:202112.06'

input:
Expand All @@ -26,6 +21,10 @@ process SENTIEON_BWAMEM {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/sentieon/dedup/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,6 @@ process SENTIEON_DEDUP {

secret 'SENTIEON_LICENSE_BASE64'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
}

container 'nf-core/sentieon:202112.06'

input:
Expand All @@ -31,6 +26,10 @@ process SENTIEON_DEDUP {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/sentieon/gvcftyper/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,6 @@ process SENTIEON_GVCFTYPER {

secret 'SENTIEON_LICENSE_BASE64'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
}

container 'nf-core/sentieon:202112.06'

input:
Expand All @@ -28,6 +23,10 @@ process SENTIEON_GVCFTYPER {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def prefix = task.ext.prefix ?: "${meta.id}"
def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/sentieon/haplotyper/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,6 @@ process SENTIEON_HAPLOTYPER {

secret 'SENTIEON_LICENSE_BASE64'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
}

container 'nf-core/sentieon:202112.06'

input:
Expand All @@ -32,6 +27,10 @@ process SENTIEON_HAPLOTYPER {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: '' // options for the driver
def args2 = task.ext.args2 ?: '' // options for the vcf generation
def args3 = task.ext.args3 ?: '' // options for the gvcf generation
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/sentieon/varcal/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,6 @@ process SENTIEON_VARCAL {

secret 'SENTIEON_LICENSE_BASE64'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Sentieon modules does not support Conda. Please use Docker / Singularity / Podman instead."
}

container 'nf-core/sentieon:202112.06'

input:
Expand All @@ -31,6 +26,10 @@ process SENTIEON_VARCAL {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Sentieon modules do not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reference_command = fasta ? "--reference $fasta " : ''
Expand Down

0 comments on commit b9172e8

Please sign in to comment.