Merge pull request nf-core#3686 from jonasscheid/nftestignore-mqc-llmstxt

jonasscheid · web-flow · commit ab6cd6a5102f · 2025-07-24T12:18:50.000+02:00
Ignore MultiQC llms.txt during pipeline nf-tests
diff --git a/.github/snapshots/adaptivecard.nf.test.snap b/.github/snapshots/adaptivecard.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/changelog.nf.test.snap b/.github/snapshots/changelog.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/ci.nf.test.snap b/.github/snapshots/ci.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/citations.nf.test.snap b/.github/snapshots/citations.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/code_linters.nf.test.snap b/.github/snapshots/code_linters.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/codespaces.nf.test.snap b/.github/snapshots/codespaces.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/documentation.nf.test.snap b/.github/snapshots/documentation.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/email.nf.test.snap b/.github/snapshots/email.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/fastqc.nf.test.snap b/.github/snapshots/fastqc.nf.test.snap
@@ -11,6 +11,7 @@
                 "multiqc",
                 "multiqc/multiqc_data",
                 "multiqc/multiqc_data/BETA-multiqc.parquet",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/github_badges.nf.test.snap b/.github/snapshots/github_badges.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/gitpod.nf.test.snap b/.github/snapshots/gitpod.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/igenomes.nf.test.snap b/.github/snapshots/igenomes.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/license.nf.test.snap b/.github/snapshots/license.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/nf_core_configs.nf.test.snap b/.github/snapshots/nf_core_configs.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/nf_schema.nf.test.snap b/.github/snapshots/nf_schema.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/rocrate.nf.test.snap b/.github/snapshots/rocrate.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/seqera_platform.nf.test.snap b/.github/snapshots/seqera_platform.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/slackreport.nf.test.snap b/.github/snapshots/slackreport.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/.github/snapshots/vscode.nf.test.snap b/.github/snapshots/vscode.nf.test.snap
@@ -38,6 +38,7 @@
                 "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt",
                 "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt",
+                "multiqc/multiqc_data/llms-full.txt",
                 "multiqc/multiqc_data/multiqc.log",
                 "multiqc/multiqc_data/multiqc_citations.txt",
                 "multiqc/multiqc_data/multiqc_data.json",
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -13,7 +13,7 @@
                     }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %}
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "c9a31c472ef2d86802eb44f27322955849859361",
                         "installed_by": ["modules"]
                     }
                     {%- endif %}
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/tags.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/tags.yml
diff --git a/nf_core/pipeline-template/tests/.nftignore b/nf_core/pipeline-template/tests/.nftignore
@@ -8,6 +8,7 @@ multiqc/multiqc_data/multiqc.log
 multiqc/multiqc_data/multiqc_data.json
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_data/multiqc_software_versions.txt
+multiqc/multiqc_data/llms-full.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
 {%- endif %}
