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FIX: remove spaces in controlfreec modules #3870

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merged 1 commit into from
Sep 26, 2023
Merged

FIX: remove spaces in controlfreec modules #3870

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4 changes: 2 additions & 2 deletions modules/nf-core/controlfreec/assesssignificance/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {

conda "bioconda::control-freec=11.6b"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
'biocontainers/control-freec:11.6b--hdbdd923_0' }"

input:
tuple val(meta), path(cnvs), path(ratio)
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4 changes: 2 additions & 2 deletions modules/nf-core/controlfreec/freec/main.nf
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Expand Up @@ -4,8 +4,8 @@ process CONTROLFREEC_FREEC {

conda "bioconda::control-freec=11.6b"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
'biocontainers/control-freec:11.6b--hdbdd923_0' }"

input:
tuple val(meta), path(mpileup_normal), path(mpileup_tumor), path(cpn_normal), path(cpn_tumor), path(minipileup_normal), path(minipileup_tumor)
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4 changes: 2 additions & 2 deletions modules/nf-core/controlfreec/freec2bed/main.nf
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Expand Up @@ -4,8 +4,8 @@ process CONTROLFREEC_FREEC2BED {

conda "bioconda::control-freec=11.6b"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
'biocontainers/control-freec:11.6b--hdbdd923_0' }"

input:
tuple val(meta), path(ratio)
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4 changes: 2 additions & 2 deletions modules/nf-core/controlfreec/freec2circos/main.nf
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Expand Up @@ -4,8 +4,8 @@ process CONTROLFREEC_FREEC2CIRCOS {

conda "bioconda::control-freec=11.6b"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
'biocontainers/control-freec:11.6b--hdbdd923_0' }"

input:
tuple val(meta), path(ratio)
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5 changes: 3 additions & 2 deletions modules/nf-core/controlfreec/makegraph/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,9 @@ process CONTROLFREEC_MAKEGRAPH {

conda "bioconda::control-freec=11.6b"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0 ':
'biocontainers/control-freec:11.6b--hdbdd923_0 ' }"
'https://depot.galaxyproject.org/singularity/control-freec:11.6b--hdbdd923_0' :
'biocontainers/control-freec:11.6b--hdbdd923_0' }"

input:
tuple val(meta), path(ratio), path(baf), val(ploidy)

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