Add exit logic for modules that dont support conda

modules/nf-core/bases2fastq/main.nf

@@ -4,6 +4,11 @@ process BASES2FASTQ {
 
     container "elembio/bases2fastq:1.1.0"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(run_manifest), path(run_dir)
 

modules/nf-core/bcl2fastq/main.nf

@@ -4,6 +4,11 @@ process BCL2FASTQ {
 
     container "nfcore/bcl2fastq:2.20.0.422"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "BCL2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
 

modules/nf-core/bclconvert/main.nf

@@ -4,6 +4,11 @@ process BCLCONVERT {
 
     container "nfcore/bclconvert:4.0.3"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "BCLCONVERT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
 

modules/nf-core/cellranger/count/main.nf

@@ -4,6 +4,11 @@ process CELLRANGER_COUNT {
 
     container "nfcore/cellranger:7.0.0"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(reads)
     path  reference

modules/nf-core/cellranger/mkfastq/main.nf

@@ -4,6 +4,11 @@ process CELLRANGER_MKFASTQ {
 
     container "nfcore/cellrangermkfastq:7.0.0"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     path bcl
     path csv

modules/nf-core/cellranger/mkgtf/main.nf

@@ -4,6 +4,11 @@ process CELLRANGER_MKGTF {
 
     container "nfcore/cellranger:7.0.0"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     path gtf
 

modules/nf-core/cellranger/mkref/main.nf

@@ -4,6 +4,11 @@ process CELLRANGER_MKREF {
 
     container "nfcore/cellranger:7.0.0"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     path fasta
     path gtf

modules/nf-core/deepvariant/main.nf

@@ -4,6 +4,11 @@ process DEEPVARIANT {
 
     container "google/deepvariant:1.4.0"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(input), path(index), path(intervals)
     path(fasta)

modules/nf-core/fastk/fastk/main.nf

@@ -5,6 +5,11 @@ process FASTK_FASTK {
     // 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_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(reads)
 

modules/nf-core/fastk/histex/main.nf

@@ -5,6 +5,11 @@ process FASTK_HISTEX {
     // 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_HISTEX module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(histogram)
 

modules/nf-core/fastk/merge/main.nf

@@ -5,6 +5,11 @@ 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)
 

modules/nf-core/fcs/fcsadaptor/main.nf

@@ -7,6 +7,11 @@ process FCS_FCSADAPTOR {
         'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-adaptor.0.2.3.sif':
         '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)
 

modules/nf-core/fcs/fcsgx/main.nf

@@ -6,6 +6,11 @@ process FCS_FCSGX {
         'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-gx.0.2.3.sif':
         'ncbi/fcs-gx: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_FCSGX module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(assembly)
     path gxdb

modules/nf-core/gatk4/cnnscorevariants/main.nf

@@ -5,6 +5,11 @@ process GATK4_CNNSCOREVARIANTS {
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
     container "broadinstitute/gatk:4.3.0.0" //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

modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf

@@ -4,6 +4,11 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY {
 
     container "broadinstitute/gatk:4.3.0.0"
 
+    // 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)
     path(contig_ploidy_table)

modules/nf-core/genescopefk/main.nf

@@ -5,6 +5,11 @@ process GENESCOPEFK {
     // 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, "GENESCOPEFK module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(fastk_histex_histogram)
 

modules/nf-core/imputeme/vcftoprs/main.nf

@@ -6,6 +6,11 @@ process IMPUTEME_VCFTOPRS {
         'https://containers.biocontainers.pro/s3/SingImgsRepo/imputeme/vv1.0.7_cv1/imputeme_vv1.0.7_cv1.img' :
         'biocontainers/imputeme:vv1.0.7_cv1' }"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        exit 1, "IMPUTEME_VCFTOPRS module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(vcf)
 

modules/nf-core/merquryfk/katcomp/main.nf

@@ -5,6 +5,11 @@ process MERQURYFK_KATCOMP {
     // 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, "MERQURYFK_KATCOMP module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(fastk1_hist), path(fastk1_ktab), path(fastk2_hist), path(fastk2_ktab)
 

modules/nf-core/merquryfk/katgc/main.nf

@@ -5,6 +5,11 @@ process MERQURYFK_KATGC {
     // 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, "MERQURYFK_KATGC module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(fastk_hist), path(fastk_ktab)
 

modules/nf-core/merquryfk/merquryfk/main.nf

@@ -5,6 +5,11 @@ process MERQURYFK_MERQURYFK {
     // 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, "MERQURYFK_MERQURYFK module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(fastk_hist), path(fastk_ktab), path(assembly)
 

modules/nf-core/merquryfk/ploidyplot/main.nf

@@ -5,6 +5,11 @@ process MERQURYFK_PLOIDYPLOT {
     // 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, "MERQURYFK_PLOIDYPLOT module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+
     input:
     tuple val(meta), path(fastk_hist), path(fastk_ktab)