Resolved merged conflicts

CDCgov · Feb 5, 2025 · b4de025 · b4de025
2 parents e2a79d2 + 99aeca0
commit b4de025
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Showing 11 changed files with 19 additions and 17 deletions.
diff --git a/modules/local/aggregate_tsvs.nf b/modules/local/aggregate_tsvs.nf
@@ -4,7 +4,7 @@ process AGGREGATE_TSVS {
     conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bionumpy:0.2.17--pyha8f3691_0  ' :
-        'quay.io/biocontainers/bionumpy' }"
+        'quay.io/biocontainers/bionumpy:0.2.17--pyha8f3691_0' }"
 
     input:
     path(individual_tsvs)

diff --git a/modules/local/graph_reconstruct.nf b/modules/local/graph_reconstruct.nf
@@ -29,7 +29,8 @@ process GRAPH_RECON {
     
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+    
         python: \$(python3 --version | sed 's/Python //g')
     END_VERSIONS
     """
-}
+}
diff --git a/modules/local/publish_contigs.nf b/modules/local/publish_contigs.nf
@@ -5,8 +5,8 @@ process PUBLISH_CONTIGS {
    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bionumpy:0.2.17--pyha8f3691_0  ' :
-        'quay.io/biocontainers/bionumpy' }"
-        
+        'quay.io/biocontainers/bionumpy:0.2.17--pyha8f3691_0' }"
+
     input:
     tuple val(meta), path(assembly)
 

diff --git a/modules/local/summarize_qc.nf b/modules/local/summarize_qc.nf
@@ -3,7 +3,7 @@ process SUMMARIZE_QC {
     conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::pandas" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
-        'quay.io/biocontainers/pandas' }"
+        'quay.io/biocontainers/pandas:1.1.5' }"
 
     input:
     path summarize_qc_files

diff --git a/modules/local/summarize_tsv.nf b/modules/local/summarize_tsv.nf
@@ -5,7 +5,7 @@ process SUMMARIZE_TSV {
    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bionumpy:0.2.17--pyha8f3691_0  ' :
-        'quay.io/biocontainers/bionumpy' }"
+        'quay.io/biocontainers/bionumpy:0.2.17--pyha8f3691_0' }"
 
     input:
     tuple val(meta), path(ivar_tsv)

diff --git a/modules/local/variant_convert.nf b/modules/local/variant_convert.nf
@@ -2,9 +2,10 @@ process VARIANT_CONVERT {
     tag "$meta.id"
     label 'process_medium'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext. singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'quay.io/biocontainers/python:3.8.3' }"
+        container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bionumpy:0.2.17--pyha8f3691_0  ' :
+        'quay.io/biocontainers/bionumpy:0.2.17--pyha8f3691_0' }"
+
 
     input:
     tuple val(meta), path(tsv)

diff --git a/modules/nf-core/modules/sratools/fasterqdump/main.nf b/modules/nf-core/modules/sratools/fasterqdump/main.nf
diff --git a/modules/nf-core/modules/sratools/prefetch/main.nf b/modules/nf-core/modules/sratools/prefetch/main.nf
diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf
diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -115,7 +115,7 @@ profiles {
     }
     docker {
         docker.enabled         = true
-        docker.userEmulation   = true
+        // docker.userEmulation   = true
         singularity.enabled    = false
         podman.enabled         = false
         shifter.enabled        = false