Update local modules with latest conda fixes

drpatelh · drpatelh · commit 00bd3937200f · 2022-12-13T22:56:09.000Z
diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf
@@ -2,7 +2,7 @@ process BEDTOOLS_GENOMECOV {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
+    conda "bioconda::bedtools=2.30.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
         'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
diff --git a/modules/local/cat_additional_fasta.nf b/modules/local/cat_additional_fasta.nf
@@ -1,7 +1,7 @@
 process CAT_ADDITIONAL_FASTA {
     tag "$add_fasta"
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc.nf
@@ -3,7 +3,7 @@ process DESEQ2_QC {
 
     // (Bio)conda packages have intentionally not been pinned to a specific version
     // This was to avoid the pipeline failing due to package conflicts whilst creating the environment when using -profile conda
-    conda (params.enable_conda ? "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap" : null)
+    conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' :
         'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"
diff --git a/modules/local/dupradar.nf b/modules/local/dupradar.nf
@@ -2,7 +2,7 @@ process DUPRADAR {
     tag "$meta.id"
     label 'process_long'
 
-    conda (params.enable_conda ? "bioconda::bioconductor-dupradar=1.18.0" : null)
+    conda "bioconda::bioconductor-dupradar=1.18.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dupradar:1.18.0--r40_1' :
         'quay.io/biocontainers/bioconductor-dupradar:1.18.0--r40_1' }"
diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
@@ -2,7 +2,7 @@ process GTF2BED {
     tag "$gtf"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::perl=5.26.2" : null)
+    conda "conda-forge::perl=5.26.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
         'quay.io/biocontainers/perl:5.26.2' }"
diff --git a/modules/local/gtf_gene_filter.nf b/modules/local/gtf_gene_filter.nf
@@ -1,7 +1,7 @@
 process GTF_GENE_FILTER {
     tag "$fasta"
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -1,7 +1,7 @@
 process MULTIQC {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
diff --git a/modules/local/multiqc_custom_biotype.nf b/modules/local/multiqc_custom_biotype.nf
@@ -1,7 +1,7 @@
 process MULTIQC_CUSTOM_BIOTYPE {
     tag "$meta.id"
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/preprocess_transcripts_fasta_gencode.nf b/modules/local/preprocess_transcripts_fasta_gencode.nf
@@ -1,7 +1,7 @@
 process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
     tag "$fasta"
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'ubuntu:20.04' }"
diff --git a/modules/local/rsem_merge_counts.nf b/modules/local/rsem_merge_counts.nf
@@ -1,7 +1,7 @@
 process RSEM_MERGE_COUNTS {
     label "process_medium"
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'ubuntu:20.04' }"
diff --git a/modules/local/salmon_summarizedexperiment.nf b/modules/local/salmon_summarizedexperiment.nf
@@ -2,7 +2,7 @@ process SALMON_SUMMARIZEDEXPERIMENT {
     tag "$tx2gene"
     label "process_medium"
 
-    conda (params.enable_conda ? "bioconda::bioconductor-summarizedexperiment=1.20.0" : null)
+    conda "bioconda::bioconductor-summarizedexperiment=1.20.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.20.0--r40_0' :
         'quay.io/biocontainers/bioconductor-summarizedexperiment:1.20.0--r40_0' }"
diff --git a/modules/local/salmon_tx2gene.nf b/modules/local/salmon_tx2gene.nf
@@ -2,7 +2,7 @@ process SALMON_TX2GENE {
     tag "$gtf"
     label "process_low"
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/salmon_tximport.nf b/modules/local/salmon_tximport.nf
@@ -1,7 +1,7 @@
 process SALMON_TXIMPORT {
     label "process_medium"
 
-    conda (params.enable_conda ? "bioconda::bioconductor-tximeta=1.8.0" : null)
+    conda "bioconda::bioconductor-tximeta=1.8.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-tximeta:1.8.0--r40_0' :
         'quay.io/biocontainers/bioconductor-tximeta:1.8.0--r40_0' }"
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'quay.io/biocontainers/python:3.9--1' }"
diff --git a/modules/local/star_align_igenomes.nf b/modules/local/star_align_igenomes.nf
@@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" : null)
+    conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
         'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
diff --git a/modules/local/star_genomegenerate_igenomes.nf b/modules/local/star_genomegenerate_igenomes.nf
@@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
     tag "$fasta"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" : null)
+    conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
         'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"
diff --git a/modules/local/umitools_prepareforrsem.nf b/modules/local/umitools_prepareforrsem.nf
@@ -2,7 +2,7 @@ process UMITOOLS_PREPAREFORRSEM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
+    conda "bioconda::umi_tools=1.1.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' :
         'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }"
