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Remove tag based include filters #17

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Merged
nvnieuwk merged 1 commit into from
Sep 30, 2026
Merged

Remove tag based include filters #17

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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -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)
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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'
}
```

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2 changes: 1 addition & 1 deletion build.gradle
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Expand Up @@ -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'
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4 changes: 0 additions & 4 deletions src/main/resources/worksheets/nfcmgg_preprocessing.yml
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Expand Up @@ -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:
Expand All @@ -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
Expand Down Expand Up @@ -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:
Expand All @@ -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:
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11 changes: 8 additions & 3 deletions tests/preprocessing_mock/main.nf.test.snap
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Expand Up @@ -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"
]
],
[
Expand Down Expand Up @@ -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"
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