Merge pull request #179 from naobservatory/harmon_fix_dev

Fixing misused labels
naobservatory · Feb 3, 2025 · fce94af · fce94af
2 parents a97711a + 2c59027
commit fce94af
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Showing 7 changed files with 10 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@
     - Added new intermediate outputs, including unfiltered viral hits and interleaved FASTQ from EXTRACT_VIRAL_READS
     - Viral hits TSV moved from `virus_hits_db.tsv.gz` to `virus_hits_filtered.tsv.gz`
     - Numerous changes to column names in viral hits TSV, mainly to improve clarity
+- Updated mislabeled processes
 
 # v2.7.0.2
 - Updated `pipeline-version.txt`

diff --git a/configs/containers.config b/configs/containers.config
@@ -107,4 +107,8 @@ process {
         // - conda-forge::file=5.46
         // - conda-forge::gzip=1.13
    }
+   withLabel: python {
+      container = "community.wave.seqera.io/library/python:3.13.1--d00663700fcc8bcf"
+
+   }
 }
diff --git a/modules/local/filterTsv/main.nf b/modules/local/filterTsv/main.nf
@@ -1,6 +1,6 @@
 // Filter a gzipped TSV to keep the first line for each combination of values in the specified columns
 process FILTER_TSV {
-    label "core_utils"
+    label "coreutils"
     label "single"
     input:
         tuple val(sample), path(tsv)

diff --git a/modules/local/headTsv/main.nf b/modules/local/headTsv/main.nf
@@ -1,6 +1,6 @@
 // Add a header line to an unheaded TSV file
 process HEAD_TSV {
-    label "core_utils"
+    label "python"
     label "single"
     input:
         tuple val(sample), path(tsv)

diff --git a/modules/local/reheadTsv/main.nf b/modules/local/reheadTsv/main.nf
@@ -1,6 +1,6 @@
 // Rename fields in a TSV header
 process REHEAD_TSV {
-    label "core_utils"
+    label "python"
     label "single"
     input:
         tuple val(sample), path(tsv)

diff --git a/modules/local/sortFile/main.nf b/modules/local/sortFile/main.nf
@@ -1,7 +1,7 @@
 // Sort a gzipped file by a user-specified key string
 // TODO: Expand to handle plaintext files
 process SORT_FILE {
-    label "core_utils"
+    label "coreutils"
     label "single"
     input:
         tuple val(sample), path(file)

diff --git a/modules/local/sortTsv/main.nf b/modules/local/sortTsv/main.nf
@@ -1,7 +1,7 @@
 // Sort a gzipped TSV by a specified column header
 // TODO: Expand to handle plaintext TSVs
 process SORT_TSV {
-    label "core_utils"
+    label "coreutils"
     label "single"
     input:
         tuple val(sample), path(tsv)