Merge pull request #19 from CarsonJM/development

Updated snapshots and removed proxy code
HoffLab · Apr 24, 2024 · d0301fe · d0301fe
2 parents 6c132e2 + 322c8a3
commit d0301fe
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Showing 7 changed files with 6 additions and 20 deletions.
diff --git a/modules/local/humann/downloadchocophlandb/main.nf b/modules/local/humann/downloadchocophlandb/main.nf
@@ -20,8 +20,6 @@ process HUMANN_DOWNLOADCHOCOPHLANDB {
     script:
     def args = task.ext.args ?: ''
     """
-    https_proxy=http://klone-dip1-A-ib:3128
-    export https_proxy
     humann_databases \\
         --download chocophlan \\
         ${chocophlan_db_version} \\

diff --git a/modules/local/humann/downloadunirefdb/main.nf b/modules/local/humann/downloadunirefdb/main.nf
@@ -19,8 +19,6 @@ process HUMANN_DOWNLOADUNIREFDB {
     script:
     def args = task.ext.args ?: ''
     """
-    https_proxy=http://klone-dip1-A-ib:3128
-    export https_proxy
     humann_databases \\
         --download uniref \\
         ${uniref_db_version} \\

diff --git a/modules/local/kneaddata/database/main.nf b/modules/local/kneaddata/database/main.nf
@@ -20,8 +20,6 @@ process KNEADDATA_DATABASE {
     script:
     def args = task.ext.args ?: ''
     """
-    https_proxy=http://klone-dip1-A-ib:3128
-    export https_proxy
     kneaddata_database \\
         --download $kneaddata_db_type bowtie2 kneaddata_${kneaddata_db_type}
 

diff --git a/modules/local/kneaddata/kneaddata/tests/main.nf.test b/modules/local/kneaddata/kneaddata/tests/main.nf.test
@@ -23,9 +23,6 @@ nextflow_process {
     test("fastq.gz") {
 
         when {
-            params {
-                max_cpus = 1
-            }
             process {
                 """
                 input[0] = Channel.of(

diff --git a/modules/nf-core/metaphlan/makedb/main.nf b/modules/nf-core/metaphlan/makedb/main.nf
diff --git a/modules/nf-core/metaphlan/metaphlan/tests/main.nf.test.snap b/modules/nf-core/metaphlan/metaphlan/tests/main.nf.test.snap
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -10,12 +10,6 @@ params {
 // Impose sensible resource limits for testing
 process {
     withName: '.*' {
-        cpus   = 4
-        memory = 15.GB
-        time   = 2.h
-    }
-
-    withName: 'KNEADDATA_KNEADDATA' {
         cpus   = 1
         memory = 15.GB
         time   = 2.h
@@ -32,3 +26,6 @@ timeline { enabled = false }
 report   { enabled = false }
 trace    { enabled = false }
 dag      { enabled = false }
+
+// Load modules test_data.config
+includeConfig 'https://github.com/nf-core/modules/raw/master/tests/config/test_data.config'