diff --git a/CHANGELOG.md b/CHANGELOG.md index e96955bb..72171997 100644 --- 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 index 844efb09..aaddf764 100644 --- 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 index 6d5afc60..44695f36 100644 --- 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 index 0ea59c40..234600a3 100644 --- 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 index 97f5a160..36f87d1c 100644 --- 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 index a94b1a19..e928da1b 100644 --- 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 index 8831fc0e..79d182e3 100644 --- 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)