Move conda-checks (fourth batch) (nf-core#3694)

Moving conda-check and replacing exit 1 with error-cmd Forcing merge because these are existing errors that can't really be fixed in the scope of this PR (@adamrtalbot will take the blame). Co-authored-by: Adam Talbot <[email protected]>
EgorGuga · Aug 7, 2023 · 8c4542e · 8c4542e
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commit 8c4542e
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diff --git a/modules/nf-core/fastk/merge/main.nf b/modules/nf-core/fastk/merge/main.nf
@@ -5,11 +5,6 @@ process FASTK_MERGE {
  // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
  container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2'
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "FASTK_MERGE module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  tuple val(meta), path(hist), path(ktab), path(prof)
 
@@ -23,6 +18,10 @@ process FASTK_MERGE {
  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 "FASTK_MERGE module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

diff --git a/modules/nf-core/fcs/fcsadaptor/main.nf b/modules/nf-core/fcs/fcsadaptor/main.nf
@@ -7,11 +7,6 @@ process FCS_FCSADAPTOR {
  'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-adaptor.0.2.3.sif':
  'docker.io/ncbi/fcs-adaptor:0.2.3' }"
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "FCS_FCSADAPTOR module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  tuple val(meta), path(assembly)
 
@@ -27,6 +22,10 @@ process FCS_FCSADAPTOR {
  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 "FCS_FCSADAPTOR module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: '--prok' // --prok || --euk
  def prefix = task.ext.prefix ?: "${meta.id}"
  def FCSADAPTOR_VERSION = '0.2.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

diff --git a/modules/nf-core/fcs/fcsgx/main.nf b/modules/nf-core/fcs/fcsgx/main.nf
@@ -6,11 +6,6 @@ process FCS_FCSGX {
  'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.4.0/fcs-gx.sif':
  'docker.io/ncbi/fcs-gx:0.4.0' }"
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "FCS_FCSGX module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  tuple val(meta), path(assembly)
  path gxdb
@@ -24,6 +19,10 @@ process FCS_FCSGX {
  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 "FCS_FCSGX module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def FCSGX_VERSION = '0.4.0'
@@ -44,6 +43,10 @@ process FCS_FCSGX {
  """
 
  stub:
+ // Exit if running this module with -profile conda / -profile mamba
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "FCS_FCSGX module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def prefix = task.ext.prefix ?: "${meta.id}"
  def FCSGX_VERSION = '0.4.0'
 

diff --git a/modules/nf-core/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf
@@ -5,11 +5,6 @@ process GATK4_CNNSCOREVARIANTS {
  //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
  container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "GATK4_CNNSCOREVARIANTS module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals)
  path fasta
@@ -27,6 +22,10 @@ process GATK4_CNNSCOREVARIANTS {
  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 "GATK4_CNNSCOREVARIANTS module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def aligned_input = aligned_input ? "--input $aligned_input" : ""

diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf
@@ -6,11 +6,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY {
  //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
  container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  tuple val(meta), path(counts), path(bed), path(exclude_beds)
  tuple val(meta2), path(ploidy_model)
@@ -25,6 +20,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY {
  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 "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: ''
  prefix = task.ext.prefix ?: "${meta.id}"
  def intervals = bed ? "--intervals ${bed}" : ""
@@ -58,6 +57,10 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY {
  """
 
  stub:
+ // Exit if running this module with -profile conda / -profile mamba
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "GATK4_DETERMINEGERMLINECONTIGPLOIDY module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  prefix = task.ext.prefix ?: "${meta.id}"
  """
  touch ${prefix}-calls

diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf
@@ -5,11 +5,6 @@ process GATK4_GERMLINECNVCALLER {
  //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
  container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  tuple val(meta), path(tsv), path(intervals), path(ploidy), path(model)
 
@@ -22,6 +17,10 @@ process GATK4_GERMLINECNVCALLER {
  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 "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def intervals_command = intervals ? "--intervals ${intervals}" : ""
@@ -53,6 +52,10 @@ process GATK4_GERMLINECNVCALLER {
  """
 
  stub:
+ // Exit if running this module with -profile conda / -profile mamba
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "GATK4_GERMLINECNVCALLER module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def prefix = task.ext.prefix ?: "${meta.id}"
  """
  mkdir -p ${prefix}-cnv-calls/${prefix}-calls

diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf
@@ -5,11 +5,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS {
  //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
  container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  tuple val(meta), path(calls), path(model), path(ploidy)
 
@@ -23,6 +18,10 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS {
  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 "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def calls_command = calls ? calls.collect{"--calls-shard-path $it"}.join(' ') : ""
@@ -51,6 +50,10 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS {
  """
 
  stub:
+ // Exit if running this module with -profile conda / -profile mamba
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def prefix = task.ext.prefix ?: "${meta.id}"
  """
  touch ${prefix}_genotyped_intervals.vcf.gz

diff --git a/modules/nf-core/spaceranger/mkgtf/main.nf b/modules/nf-core/spaceranger/mkgtf/main.nf
@@ -4,11 +4,6 @@ process SPACERANGER_MKGTF {
 
  container "docker.io/nfcore/spaceranger:2.1.0"
 
- // Exit if running this module with -profile conda / -profile mamba
- if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
- exit 1, "SPACERANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
- }
-
  input:
  path gtf
 
@@ -20,6 +15,10 @@ process SPACERANGER_MKGTF {
  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 "SPACERANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
+ }
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${gtf.baseName}.filtered"
  """