conda-safe containers, assuming nextflow pulls from docker.io happily

cancerit · Nov 6, 2024 · 26c30f3 · 26c30f3
1 parent 1fc5d7a
commit 26c30f3
Show file tree

Hide file tree

Showing 12 changed files with 11 additions and 204 deletions.
diff --git a/modules/local/crispresso2/functions.nf b/modules/local/crispresso2/functions.nf
diff --git a/modules/local/crispresso2/main.nf b/modules/local/crispresso2/main.nf
diff --git a/modules/local/crispresso2/meta.yml b/modules/local/crispresso2/meta.yml
diff --git a/modules/local/cutadapt/main.nf b/modules/local/cutadapt/main.nf
@@ -12,11 +12,8 @@ process CUTADAPT {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::cutadapt=4.4' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/cutadapt:4.4--py39hf95cd2a_1'
-    } else {
-        container 'quay.io/biocontainers/cutadapt:4.4--py39hf95cd2a_1'
-    }
+    container 'quay.io/biocontainers/cutadapt:4.4--py39hf95cd2a_1'
+
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/flash2/main.nf b/modules/local/flash2/main.nf
@@ -11,11 +11,7 @@ process FLASH2 {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::flash=2.2.00" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/flash2:2.2.00--h5bf99c6_3"
-    } else {
-        container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
-    }
+    container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/pyquest/main.nf b/modules/local/pyquest/main.nf
@@ -12,11 +12,7 @@ process PYQUEST {
 
     // Keep for when container is public
     /*
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/flash2:2.2.00--h5bf99c6_3"
-    } else {
-        container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
-    }
+    container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
     */
     container "quay.io/wtsicgp/pyquest:1.1.0"
 

diff --git a/modules/local/pyquest_library_converter/main.nf b/modules/local/pyquest_library_converter/main.nf
@@ -10,12 +10,8 @@ process TRANSFORM_LIBRARY_FOR_PYQUEST {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pyquest', meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? null : null)
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
+    conda (params.enable_conda ? "conda-forge::python=3.12.7" : null)
+    container "docker.io/python:3.12.7-alpine3.20"
 
     input:
         path(oligo_library)

diff --git a/modules/local/samtools/bam2fq/main.nf b/modules/local/samtools/bam2fq/main.nf
@@ -3,9 +3,7 @@ process SAMTOOLS_BAM2FQ {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+    container 'quay.io/biocontainers/samtools:1.15--h1170115_1'
 
     input:
     tuple val(meta), path(inputbam)

diff --git a/modules/local/seqkit_seq/main.nf b/modules/local/seqkit_seq/main.nf
@@ -13,12 +13,7 @@ process SEQKIT_SEQ {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process)+'_seq', meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
-
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
-    } else {
-        container "quay.io/biocontainers/seqkit:0.15.0--0"
-    }
+    container "quay.io/biocontainers/seqkit:0.15.0--0"
 
     input:
         tuple val(meta), path(reads)

diff --git a/modules/local/seqkit_stats/main.nf b/modules/local/seqkit_stats/main.nf
@@ -13,12 +13,7 @@ process SEQKIT_STATS {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process)+'_stats', meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
-
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
-    } else {
-        container "quay.io/biocontainers/seqkit:0.15.0--0"
-    }
+    container "quay.io/biocontainers/seqkit:0.15.0--0"
 
     input:
         tuple val(meta), path(reads)

diff --git a/modules/local/seqprep/adapter_trimming/main.nf b/modules/local/seqprep/adapter_trimming/main.nf
@@ -11,11 +11,7 @@ process SEQPREP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::seqprep=1.3.2" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqprep:1.3.2--h5bf99c6_5"
-    } else {
-        container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
-    }
+    container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/local/seqprep/read_merging/main.nf b/modules/local/seqprep/read_merging/main.nf
@@ -11,11 +11,7 @@ process SEQPREP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::seqprep=1.3.2" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqprep:1.3.2--h5bf99c6_5"
-    } else {
-        container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
-    }
+    container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
 
     input:
     tuple val(meta), path(reads)