Merge pull request #3664 from nf-core/dev

Author: mashehu

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -38,4 +38,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/tools _(eg. 1.10, 1.12.1, 1.13)_
-        * Python version _(eg. 3.11, 3.12)_
+        * Python version _(eg. 3.12, 3.13)_

.github/snapshots/adaptivecard.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
             [
                 "fastqc",
                 "fastqc/SAMPLE1_PE_1_fastqc.html",
@@ -19,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -51,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -65,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -79,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/testpipeline_software_mqc_versions.yml"

.github/snapshots/changelog.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
             [
                 "fastqc",
                 "fastqc/SAMPLE1_PE_1_fastqc.html",
@@ -19,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -51,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -65,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -79,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/testpipeline_software_mqc_versions.yml"

.github/snapshots/ci.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
             [
                 "fastqc",
                 "fastqc/SAMPLE1_PE_1_fastqc.html",
@@ -19,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -51,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -65,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -79,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/testpipeline_software_mqc_versions.yml"

.github/snapshots/citations.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
             [
                 "fastqc",
                 "fastqc/SAMPLE1_PE_1_fastqc.html",
@@ -19,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -51,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -65,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -79,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/testpipeline_software_mqc_versions.yml"

.github/snapshots/code_linters.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
             [
                 "fastqc",
                 "fastqc/SAMPLE1_PE_1_fastqc.html",
@@ -19,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -51,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -65,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -79,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/testpipeline_software_mqc_versions.yml"

.github/snapshots/codespaces.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
             [
                 "fastqc",
                 "fastqc/SAMPLE1_PE_1_fastqc.html",
@@ -19,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -51,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -65,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -79,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/testpipeline_software_mqc_versions.yml"

.github/snapshots/default.nf.test.snap

@@ -26,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -58,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -72,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -86,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/nf_core_testpipeline_software_mqc_versions.yml"
@@ -109,7 +107,7 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "24.10.5"
         },
         "timestamp": "2025-05-07T13:29:04.284923"
     }

.github/snapshots/documentation.nf.test.snap

@@ -2,7 +2,14 @@
     "-profile test": {
         "content": [
             4,
-            null,
+            {
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "Workflow": {
+                    "my-prefix/testpipeline": "v1.0.0dev"
+                }
+            },
             [
                 "fastqc",
                 "fastqc/SAMPLE1_PE_1_fastqc.html",
@@ -19,6 +26,7 @@
                 "fastqc/SAMPLE3_SE_2_fastqc.zip",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/BETA-multiqc.parquet",
                 "multiqc/multiqc_data/fastqc-status-check-heatmap.txt",
                 "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt",
                 "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt",
@@ -51,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
-                "multiqc/multiqc_plots/pdf/general_stats_table.pdf",
                 "multiqc/multiqc_plots/png",
                 "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
@@ -65,7 +72,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
-                "multiqc/multiqc_plots/png/general_stats_table.png",
                 "multiqc/multiqc_plots/svg",
                 "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
@@ -79,7 +85,6 @@
                 "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg",
-                "multiqc/multiqc_plots/svg/general_stats_table.svg",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
                 "pipeline_info/testpipeline_software_mqc_versions.yml"