Merge pull request #105 from mskcc/feature/offline

fix docker location issues
mskcc · Feb 28, 2024 · ea6d373 · ea6d373
2 parents 79f1bd2 + 12f4cc8
commit ea6d373
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Showing 12 changed files with 117 additions and 27 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -178,6 +178,7 @@ process {
             ["GRCh38","hg38"].contains(params.genome) ? 'hg38' :
             ["mm10","GRCm38"].contains(params.genome) ? 'mm10' :
             'mm39'
+        storeDir = { "${params.reference_base}/${params.genome}/arriba" }
     }
 
     withName: MERGE_CFF {
@@ -224,6 +225,10 @@ process {
         ]
     }
 
+    withName: AGFUSION_DOWNLOAD {
+        storeDir = { "${params.reference_base}/${params.genome}/agfusion" }
+    }
+
     withName: ONCOKB_FUSIONANNOTATOR {
         ext.when = params.run_oncokb_fusionannotator
         secret = ["ONCOKB_TOKEN"]

diff --git a/modules.json b/modules.json
@@ -42,7 +42,7 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
                         "installed_by": ["modules"]
                     },
                     "kallisto/index": {

diff --git a/modules/local/agfusion/batch/main.nf b/modules/local/agfusion/batch/main.nf
@@ -6,7 +6,7 @@ process AGFUSION_BATCH {
     conda 'bioconda::agfusion=1.252'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'docker://cmopipeline/agfusion:0.0.6' :
-        'docker://cmopipeline/agfusion:0.0.6' }"
+        'docker.io/cmopipeline/agfusion:0.0.6' }"
 
     input:
     tuple val(meta), path(fusions)

diff --git a/modules/local/agfusion/download/main.nf b/modules/local/agfusion/download/main.nf
@@ -5,7 +5,7 @@ process AGFUSION_DOWNLOAD {
     conda 'bioconda::agfusion=1.252'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'docker://cmopipeline/agfusion:0.0.6' :
-        'docker://cmopipeline/agfusion:0.0.6' }"
+        'docker.io/cmopipeline/agfusion:0.0.6' }"
 
     input:
     val(ensembl_release)

diff --git a/modules/local/count_features/main.nf b/modules/local/count_features/main.nf
@@ -5,7 +5,7 @@ process COUNT_FEATURES {
 /// must be using singularity 3.7+
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-rtracklayer:1.60.0--r43ha9d7317_0' :
-        'https://depot.galaxyproject.org/singularity/bioconductor-rtracklayer:1.60.0--r43ha9d7317_0' }"
+        'biocontainers/bioconductor-rtracklayer:1.60.0--r43ha9d7317_0' }"
 
     input:
     tuple val(meta), path(abundance)

diff --git a/modules/local/metafusion/main.nf b/modules/local/metafusion/main.nf
@@ -4,7 +4,7 @@ process METAFUSION {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'docker://cmopipeline/metafusion:0.0.6' :
-        'docker://cmopipeline/metafusion:0.0.6' }"
+        'docker.io/cmopipeline/metafusion:0.0.6' }"
 
     input:
     tuple val(meta), path(cff)

diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap
diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml