From 31b145742897e199684165a414dc3e7fcbe52557 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 30 Sep 2026 11:00:01 +0200 Subject: [PATCH] remove tag based include filters --- CHANGELOG.md | 4 ++++ README.md | 2 +- build.gradle | 2 +- .../resources/worksheets/nfcmgg_preprocessing.yml | 4 ---- tests/preprocessing_mock/main.nf.test.snap | 11 ++++++++--- 5 files changed, 14 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index babaf4c..39b32a6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,7 @@ +## 0.4.1 + +1. Removed tag based include filters since that doesn't make sense anymore after splitting samplesheets per tag + ## 0.4.0 1. Added a new worksheet field: `samplesheets_setting`. This field can be used to change the behaviour of the samplesheet creation. Currently this field only contains one options called `split_by` which can be used to specify a field to split on (for example on analysis tag) diff --git a/README.md b/README.md index 63dea36..d59aa36 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ To use the plugin add the following to your `nextflow.config`: ```groovy plugins { - id 'nf-cmgg@0.4.0' + id 'nf-cmgg@0.4.1' } ``` diff --git a/build.gradle b/build.gradle index 19408a2..9ecf25b 100644 --- a/build.gradle +++ b/build.gradle @@ -6,7 +6,7 @@ dependencies { implementation 'com.squareup.okhttp3:okhttp:5.3.2' } -version = '0.4.0' +version = '0.4.1' nextflowPlugin { nextflowVersion = '25.10.0' diff --git a/src/main/resources/worksheets/nfcmgg_preprocessing.yml b/src/main/resources/worksheets/nfcmgg_preprocessing.yml index 1216fa7..a038c6c 100644 --- a/src/main/resources/worksheets/nfcmgg_preprocessing.yml +++ b/src/main/resources/worksheets/nfcmgg_preprocessing.yml @@ -104,7 +104,6 @@ samplesheets: include_func: | (data.organism?.toLowerCase() == 'homo sapiens' || data.genome?.toLowerCase() == 'grch38') && data.sample_type?.toLowerCase() == 'dna' - && data.tag?.toLowerCase() in ['wes', 'wgs'] fields: sample: pool: @@ -123,7 +122,6 @@ samplesheets: include_func: | (data.organism?.toLowerCase() == 'homo sapiens' || data.genome?.toLowerCase() == 'grch38') && data.sample_type?.toLowerCase() == 'rna' - && data.tag?.toLowerCase() == 'rnaseqmdg' && data.fastq_1 != null filter_func: | data.clusters?.toLong() >= 1000000L @@ -164,7 +162,6 @@ samplesheets: include_func: | (data.organism?.toLowerCase() == 'homo sapiens' || data.genome?.toLowerCase() == 'grch38') && data.sample_type?.toLowerCase() == 'dna' - && data.tag?.toLowerCase() in ['wes'] fields: sample: batch: @@ -182,7 +179,6 @@ samplesheets: include_func: | (data.organism?.toLowerCase() == 'homo sapiens' || data.genome?.toLowerCase() == 'grch38') && data.sample_type?.toLowerCase() == 'dna' - && data.tag?.toLowerCase() in ['wes', 'wgs'] fields: sample: family: diff --git a/tests/preprocessing_mock/main.nf.test.snap b/tests/preprocessing_mock/main.nf.test.snap index c9e6b12..c053c00 100644 --- a/tests/preprocessing_mock/main.nf.test.snap +++ b/tests/preprocessing_mock/main.nf.test.snap @@ -176,8 +176,13 @@ [ "nfcmgg_exomecnv_samplesheet.yaml", [ - "[", - " ]" + "- sample: D123456WGS", + " batch: WGS_prep_M", + " family: Proband_123456", + " cram: D123456WGS.cram", + " crai: D123456WGS.cram.crai", + " bed: D123456WGS.per-base.bed.gz", + " bed_index: D123456WGS.per-base.bed.gz.csi" ] ], [ @@ -232,7 +237,7 @@ ] } ], - "timestamp": "2026-09-24T14:47:18.311821057", + "timestamp": "2026-09-30T10:57:36.189149211", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6"