nf-core · bensouthgate · Feb 17, 2023 · Feb 16, 2023 · Feb 16, 2023
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/create_bamlist.nf b/modules/local/create_bamlist.nf
@@ -2,7 +2,7 @@ process CREATE_BAMLIST {
     //tag "$meta.id"
     label "process_low"
 
-    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://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
         'biocontainers/biocontainers:v1.2.0_cv1' }"

diff --git a/modules/local/dexseq_annotation.nf b/modules/local/dexseq_annotation.nf
@@ -2,7 +2,7 @@ process DEXSEQ_ANNOTATION {
     tag "$gtf"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::htseq=2.0.2" : null)
+    conda "bioconda::htseq=2.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/htseq:2.0.2--py310ha14a713_0' :
     'quay.io/biocontainers/htseq:2.0.2--py310ha14a713_0' }"

diff --git a/modules/local/dexseq_count.nf b/modules/local/dexseq_count.nf
@@ -2,7 +2,7 @@ process DEXSEQ_COUNT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::htseq=2.0.2" : null)
+    conda "bioconda::htseq=2.0.2"
     container "${ workflow.containerEngine == 'singularity' &&am
9E12
p; !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/htseq:2.0.2--py310ha14a713_0' :
     'quay.io/biocontainers/htseq:2.0.2--py310ha14a713_0' }"

diff --git a/modules/local/dexseq_dtu.nf b/modules/local/dexseq_dtu.nf
@@ -1,7 +1,7 @@
 process DEXSEQ_DTU {
     label "process_high"
 
-    conda (params.enable_conda ? "bioconda::bioconductor-dexseq=1.36.0" : null)
+    conda "bioconda::bioconductor-dexseq=1.36.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dexseq:1.36.0--r40_0' :
         'quay.io/biocontainers/bioconductor-dexseq:1.36.0--r40_0' }"

diff --git a/modules/local/dexseq_exon.nf b/modules/local/dexseq_exon.nf
@@ -1,7 +1,7 @@
 process DEXSEQ_EXON {
     label "process_high"
 
-    conda (params.enable_conda ? "bioconda::bioconductor-dexseq=1.36.0" : null)
+    conda "bioconda::bioconductor-dexseq=1.36.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dexseq:1.36.0--r40_0' :
         'quay.io/biocontainers/bioconductor-dexseq:1.36.0--r40_0' }"

diff --git a/modules/local/drimseq_filter.nf b/modules/local/drimseq_filter.nf
@@ -1,7 +1,7 @@
 process DRIMSEQ_FILTER {
     label "process_medium"
 
-    conda (params.enable_conda ? "bioconda::bioconductor-drimseq=1.18.0" : null)
+    conda "bioconda::bioconductor-drimseq=1.18.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-drimseq:1.18.0--r40_0' :
         'quay.io/biocontainers/bioconductor-drimseq:1.18.0--r40_0' }"

diff --git a/modules/local/edger_exon.nf b/modules/local/edger_exon.nf
@@ -2,7 +2,7 @@ process EDGER_EXON {
     tag "$samplesheet"
     label "process_single"
 
-    conda (params.enable_conda ? "bioconda::bioconductor-edger=3.36.0 conda-forge::r-statmod=1.4.36" : null)
+    conda "bioconda::bioconductor-edger=3.36.0 conda-forge::r-statmod=1.4.36"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' :
         'quay.io/biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:709335c37934db1b481054cbec637c6e5b5971cb-0' }"

diff --git a/modules/local/gffread_tx2gene.nf b/modules/local/gffread_tx2gene.nf
@@ -2,7 +2,7 @@ process GFFREAD_TX2GENE {
     tag "$gtf"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
+    conda "bioconda::gffread=0.12.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' :
         'quay.io/biocontainers/gffread:0.12.1--h8b12597_0' }"

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/rmats_post.nf b/modules/local/rmats_post.nf
@@ -1,7 +1,7 @@
 process RMATS_POST {
     label "process_medium"
 
-    conda (params.enable_conda ? 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2' : null)
+    conda 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' :
         'quay.io/biocontainers/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' }"

diff --git a/modules/local/rmats_post_single.nf b/modules/local/rmats_post_single.nf
@@ -1,7 +1,7 @@
 process RMATS_POST_SINGLE {
     label "process_medium"
 
-    conda (params.enable_conda ? 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2' : null)
+    conda 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' :
         'quay.io/biocontainers/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' }"

diff --git a/modules/local/rmats_prep.nf b/modules/local/rmats_prep.nf
@@ -1,7 +1,7 @@
 process RMATS_PREP {
     label "process_medium"
 
-    conda (params.enable_conda ? 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2' : null)
+    conda 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' :
         'quay.io/biocontainers/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' }"

diff --git a/modules/local/rmats_prep_single.nf b/modules/local/rmats_prep_single.nf
@@ -1,7 +1,7 @@
 process RMATS_PREP_SINGLE {
     label "process_medium"
 
-    conda (params.enable_conda ? 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2' : null)
+    conda 'bioconda::bioconductor-pairadise=1.10 bioconda::rmats=4.1.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' :
         'quay.io/biocontainers/mulled-v2-c5a18b683684b2b5cb608213a267834373186743:1c831c11c46ebe0c54bcb67918bc35fedf1c43ee-0' }"

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -2,10 +2,10 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda "conda-forge::python=3.8.3"
+    conda "conda-forge::python=3.9.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'quay.io/biocontainers/python:3.8.3' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'quay.io/biocontainers/python:3.9--1' }"
 
     input:
     path samplesheet

diff --git a/modules/local/stager.nf b/modules/local/stager.nf
@@ -1,7 +1,7 @@
 process STAGER {
     label "process_medium"
 
-    conda (params.enable_conda ? "bioconda::bioconductor-stager=1.12.0" : null)
+    conda "bioconda::bioconductor-stager=1.12.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-stager:1.12.0--r40_0' :
         'quay.io/biocontainers/bioconductor-stager:1.12.0--r40_0' }"

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
@@ -4,7 +4,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
 
     // See https://github.com/nf-core/rnaseq/pull/835 for more details on different versions
 
-    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/suppa_clusterevents.nf b/modules/local/suppa_clusterevents.nf
@@ -3,7 +3,7 @@ process CLUSTEREVENTS {
     label 'process_high'
     stageInMode = 'copy'
 
-    conda (params.enable_conda ? "bioconda::suppa" : null)
+    conda "bioconda::suppa"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/suppa%3A2.3--py36_0' :
         'quay.io/biocontainers/suppa:2.3--py36_0' }"

diff --git a/modules/local/suppa_diffsplice.nf b/modules/local/suppa_diffsplice.nf
@@ -2,7 +2,7 @@ process DIFFSPLICE {
     tag "$tpms"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::suppa" : null)
+    conda "bioconda::suppa"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/suppa%3A2.3--py36_0' :
         'quay.io/biocontainers/suppa:2.3--py_2' }"

diff --git a/modules/local/suppa_generateevents.nf b/modules/local/suppa_generateevents.nf
@@ -2,7 +2,7 @@ process GENERATE_EVENTS {
     tag "$gtf"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::suppa" : null)
+    conda "bioconda::suppa"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/suppa%3A2.3--py36_0' :
         'quay.io/biocontainers/suppa:2.3--py36_0' }"

diff --git a/modules/local/suppa_psiperevent.nf b/modules/local/suppa_psiperevent.nf
@@ -2,7 +2,7 @@ process PSIPEREVENT {
     tag "$tpm"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::suppa" : null)
+    conda "bioconda::suppa"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/suppa%3A2.3--py36_0' :
         'quay.io/biocontainers/suppa:2.3--py36_0' }"

diff --git a/modules/local/suppa_psiperisoform.nf b/modules/local/suppa_psiperisoform.nf
@@ -2,7 +2,7 @@ process PSIPERISOFORM {
     tag "$tpm"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::suppa" : null)
+    conda "bioconda::suppa"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/suppa%3A2.3--py36_0' :
         'quay.io/biocontainers/suppa:2.3--py36_0' }"

diff --git a/modules/local/suppa_split_files.nf b/modules/local/suppa_split_files.nf
@@ -2,7 +2,7 @@ process SPLIT_FILES {
     tag "$tpm_psi"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::r-base=4.0.3" : null)
+    conda "conda-forge::r-base=4.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ad9dd5f398966bf899ae05f8e7c54d0fb10cdfa7:05678da05b8e5a7a5130e90a9f9a6c585b965afa-0':
         'quay.io/biocontainers/r-base:3.4.2' }"

diff --git a/modules/local/tximport.nf b/modules/local/tximport.nf
@@ -2,7 +2,7 @@ process TXIMPORT {
     tag "$gtf"
     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/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf
diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
diff --git a/modules/nf-core/rsem/preparereference/main.nf b/modules/nf-core/rsem/preparereference/main.nf
diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf
diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf
diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf
diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf