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Add round_digits to decoupler and avoid sorting by topTable in dream (#12114)
* update dream * allow round_digits in decoupler
1 parent 2e0ae2f commit 95a5fb2

4 files changed

Lines changed: 40 additions & 167 deletions

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‎modules/nf-core/decoupler/decoupler/templates/decoupler.py‎

Lines changed: 11 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -45,6 +45,9 @@ def parse_ext_args(args_string: str):
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)
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parser.add_argument("--features_id_col", type=str, default="gene_id", help="Column name for feature IDs")
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parser.add_argument("--features_symbol_col", type=str, default="gene_name", help="Column name for feature symbols")
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parser.add_argument(
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"--round_digits", type=int, default=None, help="Number of digits to round numeric output columns"
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)
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return parser.parse_args(args_list)
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@@ -88,10 +91,15 @@ def parse_ext_args(args_string: str):
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for result in results:
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# Save table
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results[result].to_csv("${task.ext.prefix}" + "_" + result + "_decoupler.tsv", sep="\t")
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contrast_name = results[result].index[0]
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result_df = results[result].copy()
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if parsed_args.round_digits is not None:
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numeric_columns = result_df.select_dtypes(include="number").columns
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result_df[numeric_columns] = result_df[numeric_columns].round(parsed_args.round_digits)
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result_df.to_csv("${task.ext.prefix}" + "_" + result + "_decoupler.tsv", sep="\t")
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contrast_name = result_df.index[0]
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plt.figure(figsize=(8, 6))
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dc.plot_barplot(results[result], contrast_name, top=25, vertical=False)
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dc.plot_barplot(result_df, contrast_name, top=25, vertical=False)
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plt.savefig("${task.ext.prefix}" + "_" + result + "_decoupler_plot.png", dpi=300, bbox_inches="tight")
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plt.close()
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‎modules/nf-core/variancepartition/dream/templates/dream.R‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -340,9 +340,12 @@ fitmm <- eBayes(fitmm, proportion = opt\$proportion,
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winsor.tail.p = winsor_tail_p_vals)
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results <- topTable(fitmm, coef = top_table_coef, number = Inf,
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adjust.method = opt\$adjust.method,
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sort.by = "none", adjust.method = opt\$adjust.method,
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p.value = opt\$p.value, lfc = opt\$lfc, confint = opt\$confint)
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feature_order <- rownames(countMatrix)
347+
results <- results[feature_order[feature_order %in% rownames(results)], , drop = FALSE]
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results\$gene_id <- rownames(results)
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results <- results[, c("gene_id", setdiff(names(results), "gene_id"))]
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‎modules/nf-core/variancepartition/dream/tests/main.nf.test.snap‎

Lines changed: 21 additions & 159 deletions
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@@ -15,11 +15,11 @@
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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]
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],
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"timestamp": "2025-12-23T18:57:51.598745459",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
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},
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"timestamp": "2025-12-23T18:57:51.598745459"
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}
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},
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"RNAseq - Feature Counts - formula + comparison contrast string - interaction": {
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"content": [
@@ -37,11 +37,11 @@
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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]
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],
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"timestamp": "2025-12-26T15:10:51.980662299",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
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},
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"timestamp": "2025-12-26T15:10:51.980662299"
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}
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},
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"Mus musculus - contrasts - matrix - no formula": {
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"content": [
@@ -61,149 +61,11 @@
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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]
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],
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"timestamp": "2025-12-16T15:52:08.047223666",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-16T15:52:08.047223666"
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},
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"Mus musculus - expression table - contrasts + blocking factors": {
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"content": [
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{
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"0": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.results.tsv:md5,df0717ddf702543c375c1a5f4eae3fd7"
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]
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],
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"1": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.model.txt:md5,7103206474aa480ffd9cec149263489f"
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]
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],
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"2": [
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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],
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"model": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.model.txt:md5,7103206474aa480ffd9cec149263489f"
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]
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],
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"results": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.results.tsv:md5,df0717ddf702543c375c1a5f4eae3fd7"
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]
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],
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"versions": [
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-12-16T19:59:57.947286403"
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},
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"Mus musculus - expression table - contrasts + blocking factors stub": {
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"content": [
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{
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"0": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"2": [
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"versions.yml:md5,03b686ec8c67a91501ebb2b2a5234e77"
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],
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"model": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.model.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"results": [
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[
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{
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"id": "treatment_mCherry_hND6",
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"variable": "treatment",
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"reference": "mCherry",
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"target": "hND6",
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"blocking_factors": "sample_number",
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"formula": "~ treatment + (1 | sample_number)"
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},
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"treatment_mCherry_hND6.dream.results.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions": [
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"versions.yml:md5,03b686ec8c67a91501ebb2b2a5234e77"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-11-10T16:18:37.294899756"
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}
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},
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"Mus musculus - expression table - contrasts + formula + weighted comparison contrast string": {
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"content": [
@@ -221,11 +83,11 @@
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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]
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],
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"timestamp": "2025-12-23T18:57:42.761838155",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
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},
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"timestamp": "2025-12-23T18:57:42.761838155"
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}
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},
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"Mus musculus - expression table - contrasts + formula + comparison contrast string - no intercept stub": {
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"content": [
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]
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}
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],
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"timestamp": "2026-01-13T15:35:07.121696674",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
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},
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"timestamp": "2026-01-13T15:35:07.121696674"
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}
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},
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"RNAseq - Voom - Feature Counts - formula + comparison contrast string - interaction": {
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"content": [
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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],
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"timestamp": "2026-01-13T15:53:31.743589111",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
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},
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"timestamp": "2026-01-13T15:53:31.743589111"
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}
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},
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"RNAseq - Feature Counts - formula + comparison contrast string - interaction with seed": {
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"content": [
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"formula": "~ genotype * treatment",
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"comparison": "genotypeWT - treatmentTreated"
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},
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"genotype_WT_KO_treatment_Control_Treated.dream.results.tsv:md5,90a06e6b4945c706025582a4c9fddf2c"
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"genotype_WT_KO_treatment_Control_Treated.dream.results.tsv:md5,1d4c862325e4f5228c6277344c2f6b7d"
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]
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],
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"1": [
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"formula": "~ genotype * treatment",
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"comparison": "genotypeWT - treatmentTreated"
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"genotype_WT_KO_treatment_Control_Treated.dream.results.tsv:md5,90a06e6b4945c706025582a4c9fddf2c"
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"genotype_WT_KO_treatment_Control_Treated.dream.results.tsv:md5,1d4c862325e4f5228c6277344c2f6b7d"
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]
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],
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"versions": [
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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]
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}
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],
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"timestamp": "2026-06-19T15:01:27.265474319",
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.3"
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},
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"timestamp": "2026-05-07T19:32:24.587570625"
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"nf-test": "0.9.5",
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"nextflow": "26.04.4"
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}
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"Mus musculus - expression table - contrasts + formula + comparison contrast string": {
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"content": [
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"versions.yml:md5,fc1f26eb2194018e99fc2916332676b7"
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"timestamp": "2025-12-26T15:11:01.472042429",
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"nf-test": "0.9.3",
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"nextflow": "25.04.2"
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"timestamp": "2025-12-26T15:11:01.472042429"
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}
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}
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}
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}

‎subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap‎

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"fc_threshold": 1.5,
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"stat_threshold": 0.05
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},
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"treatment_mCherry_hND6_test_filtered.tsv:md5,68017f084a058f7502415f8aecda42ee"
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"treatment_mCherry_hND6_test_filtered.tsv:md5,91242680e2b4b312802dc7a65f397773"
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"timestamp": "2026-05-20T14:15:35.598682502",
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"timestamp": "2026-06-19T15:05:15.4675545",
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"nf-test": "0.9.5",
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"nextflow": "26.04.1"
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"nextflow": "26.04.4"
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"deseq2 - mouse - basic": {
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}
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}

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