Add nf-test: test_alternativepreprocessing by jfy133 · Pull Request #695 · nf-core/taxprofiler

jfy133 · 2026-03-01T13:51:40Z

Directory structure to check:

results_altpreprocessing/
├── adapterremoval
│   ├── 2612_ERR5766176_B.settings
│   ├── 2612_ERR5766176.settings
│   └── 2613_ERR5766181.settings
├── bbduk
│   ├── 2612_ERR5766176_B.bbduk.log
│   ├── 2612_ERR5766176.bbduk.log
│   └── 2613_ERR5766181.bbduk.log
├── bowtie2
│   └── align
│       ├── 2612_ERR5766176_B.bowtie2.log
│       ├── 2612_ERR5766176.bowtie2.log
│       └── 2613_ERR5766181.bowtie2.log
├── fastqc
│   ├── processed
│   │   ├── 2612_ERR5766176_B_processed_1_fastqc.html
│   │   ├── 2612_ERR5766176_B_processed_1_fastqc.zip
│   │   ├── 2612_ERR5766176_B_processed_2_fastqc.html
│   │   ├── 2612_ERR5766176_B_processed_2_fastqc.zip
│   │   ├── 2612_ERR5766176_processed_1_fastqc.html
│   │   ├── 2612_ERR5766176_processed_1_fastqc.zip
│   │   ├── 2612_ERR5766176_processed_2_fastqc.html
│   │   ├── 2612_ERR5766176_processed_2_fastqc.zip
│   │   ├── 2613_ERR5766181_processed_1_fastqc.html
│   │   ├── 2613_ERR5766181_processed_1_fastqc.zip
│   │   ├── 2613_ERR5766181_processed_2_fastqc.html
│   │   ├── 2613_ERR5766181_processed_2_fastqc.zip
│   │   ├── ERR3201952_ERR3201952_processed_fastqc.html
│   │   └── ERR3201952_ERR3201952_processed_fastqc.zip
│   └── raw
│       ├── 2612_ERR5766176_B_raw_1_fastqc.html
│       ├── 2612_ERR5766176_B_raw_1_fastqc.zip
│       ├── 2612_ERR5766176_B_raw_2_fastqc.html
│       ├── 2612_ERR5766176_B_raw_2_fastqc.zip
│       ├── 2612_ERR5766176_raw_1_fastqc.html
│       ├── 2612_ERR5766176_raw_1_fastqc.zip
│       ├── 2612_ERR5766176_raw_2_fastqc.html
│       ├── 2612_ERR5766176_raw_2_fastqc.zip
│       ├── 2613_ERR5766181_raw_1_fastqc.html
│       ├── 2613_ERR5766181_raw_1_fastqc.zip
│       ├── 2613_ERR5766181_raw_2_fastqc.html
│       ├── 2613_ERR5766181_raw_2_fastqc.zip
│       ├── ERR3201952_ERR3201952_raw_fastqc.html
│       └── ERR3201952_ERR3201952_raw_fastqc.zip
├── filtlong
│   └── ERR3201952_ERR3201952_filtered.log
├── kaiju
│   ├── db5
│   │   ├── 2611_db5.kaijutable.txt
│   │   ├── 2611_db5.kaiju.tsv
│   │   ├── 2612_db5.kaijutable.txt
│   │   ├── 2612_db5.kaiju.tsv
│   │   ├── 2613_db5.kaijutable.txt
│   │   └── 2613_db5.kaiju.tsv
│   ├── db6
│   │   ├── 2614_db6.kaijutable.txt
│   │   ├── 2614_db6.kaiju.tsv
│   │   ├── ERR3201952_db6.kaijutable.txt
│   │   └── ERR3201952_db6.kaiju.tsv
│   └── db7
│       ├── 2611_db7.kaijutable.txt
│       ├── 2611_db7.kaiju.tsv
│       ├── 2612_db7.kaijutable.txt
│       ├── 2612_db7.kaiju.tsv
│       ├── 2613_db7.kaijutable.txt
│       ├── 2613_db7.kaiju.tsv
│       ├── 2614_db7.kaijutable.txt
│       ├── 2614_db7.kaiju.tsv
│       ├── ERR3201952_db7.kaijutable.txt
│       └── ERR3201952_db7.kaiju.tsv
├── kraken2
│   └── db2
│       ├── 2611_db2.kraken2.kraken2.report.txt
│       ├── 2612_db2.kraken2.kraken2.report.txt
│       └── 2613_db2.kraken2.kraken2.report.txt
├── multiqc
│   ├── multiqc_data
│   │   ├── ar_length_count_plot_All.txt
│   │   ├── ar_length_count_plot_Discarded.txt
│   │   ├── ar_length_count_plot_Mate1.txt
│   │   ├── ar_length_count_plot_Mate2.txt
│   │   ├── ar_length_count_plot_Singleton.txt
│   │   ├── ar_retained_plot.txt
│   │   ├── bbduk-filtered-barplot_Bases.txt
│   │   ├── bbduk-filtered-barplot_Reads.txt
│   │   ├── bbduk.txt
│   │   ├── bowtie2_pe_plot.txt
│   │   ├── fastqc-1_adapter_content_plot.txt
│   │   ├── fastqc-1_per_base_n_content_plot.txt
│   │   ├── fastqc-1_per_base_sequence_quality_plot.txt
│   │   ├── fastqc-1_per_sequence_gc_content_plot_Counts.txt
│   │   ├── fastqc-1_per_sequence_gc_content_plot_Percentages.txt
│   │   ├── fastqc-1_per_sequence_quality_scores_plot.txt
│   │   ├── fastqc-1_sequence_counts_plot.txt
│   │   ├── fastqc-1_sequence_duplication_levels_plot.txt
│   │   ├── fastqc-1-status-check-heatmap.txt
│   │   ├── fastqc_adapter_content_plot.txt
│   │   ├── fastqc_per_base_n_content_plot.txt
│   │   ├── fastqc_per_base_sequence_quality_plot.txt
│   │   ├── fastqc_per_sequence_gc_content_plot_Counts.txt
│   │   ├── fastqc_per_sequence_gc_content_plot_Percentages.txt
│   │   ├── fastqc_per_sequence_quality_scores_plot.txt
│   │   ├── fastqc_sequence_counts_plot.txt
│   │   ├── fastqc_sequence_duplication_levels_plot.txt
│   │   ├── fastqc_sequence_length_distribution_plot.txt
│   │   ├── fastqc-status-check-heatmap.txt
│   │   ├── filtlong.txt
│   │   ├── kaiju-topfive-plot.txt
│   │   ├── kraken-top-n-plot_Class.txt
│   │   ├── kraken-top-n-plot_Domain.txt
│   │   ├── kraken-top-n-plot_Family.txt
│   │   ├── kraken-top-n-plot_Genus.txt
│   │   ├── kraken-top-n-plot_Kingdom.txt
│   │   ├── kraken-top-n-plot_Order.txt
│   │   ├── kraken-top-n-plot_Phylum.txt
│   │   ├── kraken-top-n-plot_Species.txt
│   │   ├── kraken-top-n-plot_Unclassified.txt
│   │   ├── llms-full.txt
│   │   ├── multiqc_adapter_removal.txt
│   │   ├── multiqc_bowtie2.txt
│   │   ├── multiqc_citations.txt
│   │   ├── multiqc_data.json
│   │   ├── multiqc_fastqc_fastqc-1.txt
│   │   ├── multiqc_fastqc.txt
│   │   ├── multiqc_general_stats.txt
│   │   ├── multiqc_kaiju_species.txt
│   │   ├── multiqc_kraken.txt
│   │   ├── multiqc.log
│   │   ├── multiqc.parquet
│   │   ├── multiqc_samtools_stats.txt
│   │   ├── multiqc_software_versions.txt
│   │   ├── multiqc_sources.txt
│   │   ├── porechop-endtrim-barplot.txt
│   │   ├── porechop-middlesplit-barplot.txt
│   │   ├── porechop_porechop.txt
│   │   ├── porechop-starttrim-barplot.txt
│   │   ├── samtools_alignment_plot.txt
│   │   └── samtools-stats-dp.txt
│   ├── multiqc_plots
│   │   ├── pdf
│   │   │   ├── ar_length_count_plot_All.pdf
│   │   │   ├── ar_length_count_plot_Discarded.pdf
│   │   │   ├── ar_length_count_plot_Mate1.pdf
│   │   │   ├── ar_length_count_plot_Mate2.pdf
│   │   │   ├── ar_length_count_plot_Singleton.pdf
│   │   │   ├── ar_retained_plot-cnt.pdf
│   │   │   ├── ar_retained_plot-pct.pdf
│   │   │   ├── bbduk-filtered-barplot_Bases-cnt.pdf
│   │   │   ├── bbduk-filtered-barplot_Bases-pct.pdf
│   │   │   ├── bbduk-filtered-barplot_Reads-cnt.pdf
│   │   │   ├── bbduk-filtered-barplot_Reads-pct.pdf
│   │   │   ├── bowtie2_pe_plot-cnt.pdf
│   │   │   ├── bowtie2_pe_plot-pct.pdf
│   │   │   ├── fastqc-1_adapter_content_plot.pdf
│   │   │   ├── fastqc-1_per_base_n_content_plot.pdf
│   │   │   ├── fastqc-1_per_base_sequence_quality_plot.pdf
│   │   │   ├── fastqc-1_per_sequence_gc_content_plot_Counts.pdf
│   │   │   ├── fastqc-1_per_sequence_gc_content_plot_Percentages.pdf
│   │   │   ├── fastqc-1_per_sequence_quality_scores_plot.pdf
│   │   │   ├── fastqc-1_sequence_counts_plot-cnt.pdf
│   │   │   ├── fastqc-1_sequence_counts_plot-pct.pdf
│   │   │   ├── fastqc-1_sequence_duplication_levels_plot.pdf
│   │   │   ├── fastqc_adapter_content_plot.pdf
│   │   │   ├── fastqc_per_base_n_content_plot.pdf
│   │   │   ├── fastqc_per_base_sequence_quality_plot.pdf
│   │   │   ├── fastqc_per_sequence_gc_content_plot_Counts.pdf
│   │   │   ├── fastqc_per_sequence_gc_content_plot_Percentages.pdf
│   │   │   ├── fastqc_per_sequence_quality_scores_plot.pdf
│   │   │   ├── fastqc_sequence_counts_plot-cnt.pdf
│   │   │   ├── fastqc_sequence_counts_plot-pct.pdf
│   │   │   ├── fastqc_sequence_duplication_levels_plot.pdf
│   │   │   ├── fastqc_sequence_length_distribution_plot.pdf
│   │   │   ├── kaiju-topfive-plot-cnt.pdf
│   │   │   ├── kaiju-topfive-plot-pct.pdf
│   │   │   ├── kraken-top-n-plot_Class-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Class-pct.pdf
│   │   │   ├── kraken-top-n-plot_Domain-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Domain-pct.pdf
│   │   │   ├── kraken-top-n-plot_Family-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Family-pct.pdf
│   │   │   ├── kraken-top-n-plot_Genus-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Genus-pct.pdf
│   │   │   ├── kraken-top-n-plot_Kingdom-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Kingdom-pct.pdf
│   │   │   ├── kraken-top-n-plot_Order-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Order-pct.pdf
│   │   │   ├── kraken-top-n-plot_Phylum-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Phylum-pct.pdf
│   │   │   ├── kraken-top-n-plot_Species-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Species-pct.pdf
│   │   │   ├── kraken-top-n-plot_Unclassified-cnt.pdf
│   │   │   ├── kraken-top-n-plot_Unclassified-pct.pdf
│   │   │   ├── porechop-endtrim-barplot-cnt.pdf
│   │   │   ├── porechop-endtrim-barplot-pct.pdf
│   │   │   ├── porechop-middlesplit-barplot-cnt.pdf
│   │   │   ├── porechop-middlesplit-barplot-pct.pdf
│   │   │   ├── porechop-starttrim-barplot-cnt.pdf
│   │   │   ├── porechop-starttrim-barplot-pct.pdf
│   │   │   ├── samtools_alignment_plot-cnt.pdf
│   │   │   ├── samtools_alignment_plot-pct.pdf
│   │   │   └── samtools-stats-dp.pdf
│   │   ├── png
│   │   │   ├── ar_length_count_plot_All.png
│   │   │   ├── ar_length_count_plot_Discarded.png
│   │   │   ├── ar_length_count_plot_Mate1.png
│   │   │   ├── ar_length_count_plot_Mate2.png
│   │   │   ├── ar_length_count_plot_Singleton.png
│   │   │   ├── ar_retained_plot-cnt.png
│   │   │   ├── ar_retained_plot-pct.png
│   │   │   ├── bbduk-filtered-barplot_Bases-cnt.png
│   │   │   ├── bbduk-filtered-barplot_Bases-pct.png
│   │   │   ├── bbduk-filtered-barplot_Reads-cnt.png
│   │   │   ├── bbduk-filtered-barplot_Reads-pct.png
│   │   │   ├── bowtie2_pe_plot-cnt.png
│   │   │   ├── bowtie2_pe_plot-pct.png
│   │   │   ├── fastqc-1_adapter_content_plot.png
│   │   │   ├── fastqc-1_per_base_n_content_plot.png
│   │   │   ├── fastqc-1_per_base_sequence_quality_plot.png
│   │   │   ├── fastqc-1_per_sequence_gc_content_plot_Counts.png
│   │   │   ├── fastqc-1_per_sequence_gc_content_plot_Percentages.png
│   │   │   ├── fastqc-1_per_sequence_quality_scores_plot.png
│   │   │   ├── fastqc-1_sequence_counts_plot-cnt.png
│   │   │   ├── fastqc-1_sequence_counts_plot-pct.png
│   │   │   ├── fastqc-1_sequence_duplication_levels_plot.png
│   │   │   ├── fastqc_adapter_content_plot.png
│   │   │   ├── fastqc_per_base_n_content_plot.png
│   │   │   ├── fastqc_per_base_sequence_quality_plot.png
│   │   │   ├── fastqc_per_sequence_gc_content_plot_Counts.png
│   │   │   ├── fastqc_per_sequence_gc_content_plot_Percentages.png
│   │   │   ├── fastqc_per_sequence_quality_scores_plot.png
│   │   │   ├── fastqc_sequence_counts_plot-cnt.png
│   │   │   ├── fastqc_sequence_counts_plot-pct.png
│   │   │   ├── fastqc_sequence_duplication_levels_plot.png
│   │   │   ├── fastqc_sequence_length_distribution_plot.png
│   │   │   ├── kaiju-topfive-plot-cnt.png
│   │   │   ├── kaiju-topfive-plot-pct.png
│   │   │   ├── kraken-top-n-plot_Class-cnt.png
│   │   │   ├── kraken-top-n-plot_Class-pct.png
│   │   │   ├── kraken-top-n-plot_Domain-cnt.png
│   │   │   ├── kraken-top-n-plot_Domain-pct.png
│   │   │   ├── kraken-top-n-plot_Family-cnt.png
│   │   │   ├── kraken-top-n-plot_Family-pct.png
│   │   │   ├── kraken-top-n-plot_Genus-cnt.png
│   │   │   ├── kraken-top-n-plot_Genus-pct.png
│   │   │   ├── kraken-top-n-plot_Kingdom-cnt.png
│   │   │   ├── kraken-top-n-plot_Kingdom-pct.png
│   │   │   ├── kraken-top-n-plot_Order-cnt.png
│   │   │   ├── kraken-top-n-plot_Order-pct.png
│   │   │   ├── kraken-top-n-plot_Phylum-cnt.png
│   │   │   ├── kraken-top-n-plot_Phylum-pct.png
│   │   │   ├── kraken-top-n-plot_Species-cnt.png
│   │   │   ├── kraken-top-n-plot_Species-pct.png
│   │   │   ├── kraken-top-n-plot_Unclassified-cnt.png
│   │   │   ├── kraken-top-n-plot_Unclassified-pct.png
│   │   │   ├── porechop-endtrim-barplot-cnt.png
│   │   │   ├── porechop-endtrim-barplot-pct.png
│   │   │   ├── porechop-middlesplit-barplot-cnt.png
│   │   │   ├── porechop-middlesplit-barplot-pct.png
│   │   │   ├── porechop-starttrim-barplot-cnt.png
│   │   │   ├── porechop-starttrim-barplot-pct.png
│   │   │   ├── samtools_alignment_plot-cnt.png
│   │   │   ├── samtools_alignment_plot-pct.png
│   │   │   └── samtools-stats-dp.png
│   │   └── svg
│   │       ├── ar_length_count_plot_All.svg
│   │       ├── ar_length_count_plot_Discarded.svg
│   │       ├── ar_length_count_plot_Mate1.svg
│   │       ├── ar_length_count_plot_Mate2.svg
│   │       ├── ar_length_count_plot_Singleton.svg
│   │       ├── ar_retained_plot-cnt.svg
│   │       ├── ar_retained_plot-pct.svg
│   │       ├── bbduk-filtered-barplot_Bases-cnt.svg
│   │       ├── bbduk-filtered-barplot_Bases-pct.svg
│   │       ├── bbduk-filtered-barplot_Reads-cnt.svg
│   │       ├── bbduk-filtered-barplot_Reads-pct.svg
│   │       ├── bowtie2_pe_plot-cnt.svg
│   │       ├── bowtie2_pe_plot-pct.svg
│   │       ├── fastqc-1_adapter_content_plot.svg
│   │       ├── fastqc-1_per_base_n_content_plot.svg
│   │       ├── fastqc-1_per_base_sequence_quality_plot.svg
│   │       ├── fastqc-1_per_sequence_gc_content_plot_Counts.svg
│   │       ├── fastqc-1_per_sequence_gc_content_plot_Percentages.svg
│   │       ├── fastqc-1_per_sequence_quality_scores_plot.svg
│   │       ├── fastqc-1_sequence_counts_plot-cnt.svg
│   │       ├── fastqc-1_sequence_counts_plot-pct.svg
│   │       ├── fastqc-1_sequence_duplication_levels_plot.svg
│   │       ├── fastqc_adapter_content_plot.svg
│   │       ├── fastqc_per_base_n_content_plot.svg
│   │       ├── fastqc_per_base_sequence_quality_plot.svg
│   │       ├── fastqc_per_sequence_gc_content_plot_Counts.svg
│   │       ├── fastqc_per_sequence_gc_content_plot_Percentages.svg
│   │       ├── fastqc_per_sequence_quality_scores_plot.svg
│   │       ├── fastqc_sequence_counts_plot-cnt.svg
│   │       ├── fastqc_sequence_counts_plot-pct.svg
│   │       ├── fastqc_sequence_duplication_levels_plot.svg
│   │       ├── fastqc_sequence_length_distribution_plot.svg
│   │       ├── kaiju-topfive-plot-cnt.svg
│   │       ├── kaiju-topfive-plot-pct.svg
│   │       ├── kraken-top-n-plot_Class-cnt.svg
│   │       ├── kraken-top-n-plot_Class-pct.svg
│   │       ├── kraken-top-n-plot_Domain-cnt.svg
│   │       ├── kraken-top-n-plot_Domain-pct.svg
│   │       ├── kraken-top-n-plot_Family-cnt.svg
│   │       ├── kraken-top-n-plot_Family-pct.svg
│   │       ├── kraken-top-n-plot_Genus-cnt.svg
│   │       ├── kraken-top-n-plot_Genus-pct.svg
│   │       ├── kraken-top-n-plot_Kingdom-cnt.svg
│   │       ├── kraken-top-n-plot_Kingdom-pct.svg
│   │       ├── kraken-top-n-plot_Order-cnt.svg
│   │       ├── kraken-top-n-plot_Order-pct.svg
│   │       ├── kraken-top-n-plot_Phylum-cnt.svg
│   │       ├── kraken-top-n-plot_Phylum-pct.svg
│   │       ├── kraken-top-n-plot_Species-cnt.svg
│   │       ├── kraken-top-n-plot_Species-pct.svg
│   │       ├── kraken-top-n-plot_Unclassified-cnt.svg
│   │       ├── kraken-top-n-plot_Unclassified-pct.svg
│   │       ├── porechop-endtrim-barplot-cnt.svg
│   │       ├── porechop-endtrim-barplot-pct.svg
│   │       ├── porechop-middlesplit-barplot-cnt.svg
│   │       ├── porechop-middlesplit-barplot-pct.svg
│   │       ├── porechop-starttrim-barplot-cnt.svg
│   │       ├── porechop-starttrim-barplot-pct.svg
│   │       ├── samtools_alignment_plot-cnt.svg
│   │       ├── samtools_alignment_plot-pct.svg
│   │       └── samtools-stats-dp.svg
│   └── multiqc_report.html
├── pipeline_info
│   ├── execution_report_2026-03-01_13-15-35.html
│   ├── execution_report_2026-03-01_13-24-00.html
│   ├── execution_report_2026-03-01_13-26-31.html
│   ├── execution_report_2026-03-01_13-28-50.html
│   ├── execution_report_2026-03-01_13-32-27.html
│   ├── execution_report_2026-03-01_13-35-51.html
│   ├── execution_report_2026-03-01_13-38-01.html
│   ├── execution_report_2026-03-01_13-40-19.html
│   ├── execution_report_2026-03-01_13-40-55.html
│   ├── execution_timeline_2026-03-01_13-15-35.html
│   ├── execution_timeline_2026-03-01_13-24-00.html
│   ├── execution_timeline_2026-03-01_13-26-31.html
│   ├── execution_timeline_2026-03-01_13-28-50.html
│   ├── execution_timeline_2026-03-01_13-32-27.html
│   ├── execution_timeline_2026-03-01_13-35-51.html
│   ├── execution_timeline_2026-03-01_13-38-01.html
│   ├── execution_timeline_2026-03-01_13-40-19.html
│   ├── execution_timeline_2026-03-01_13-40-55.html
│   ├── execution_trace_2026-03-01_13-15-35.txt
│   ├── execution_trace_2026-03-01_13-24-00.txt
│   ├── execution_trace_2026-03-01_13-26-31.txt
│   ├── execution_trace_2026-03-01_13-28-50.txt
│   ├── execution_trace_2026-03-01_13-32-27.txt
│   ├── execution_trace_2026-03-01_13-35-51.txt
│   ├── execution_trace_2026-03-01_13-38-01.txt
│   ├── execution_trace_2026-03-01_13-40-19.txt
│   ├── execution_trace_2026-03-01_13-40-55.txt
│   ├── nf_core_taxprofiler_software_mqc_versions.yml
│   ├── params_2026-03-01_13-15-46.json
│   ├── params_2026-03-01_13-24-11.json
│   ├── params_2026-03-01_13-26-42.json
│   ├── params_2026-03-01_13-29-01.json
│   ├── params_2026-03-01_13-32-37.json
│   ├── params_2026-03-01_13-36-01.json
│   ├── params_2026-03-01_13-38-12.json
│   ├── params_2026-03-01_13-40-31.json
│   ├── params_2026-03-01_13-41-04.json
│   ├── pipeline_dag_2026-03-01_13-15-35.html
│   ├── pipeline_dag_2026-03-01_13-24-00.html
│   ├── pipeline_dag_2026-03-01_13-26-31.html
│   ├── pipeline_dag_2026-03-01_13-28-50.html
│   ├── pipeline_dag_2026-03-01_13-32-27.html
│   ├── pipeline_dag_2026-03-01_13-35-51.html
│   ├── pipeline_dag_2026-03-01_13-38-01.html
│   ├── pipeline_dag_2026-03-01_13-40-19.html
│   └── pipeline_dag_2026-03-01_13-40-55.html
├── porechop
│   └── ERR3201952_ERR3201952_porechop.log
└── samtools
    └── stats
        ├── 2612_ERR5766176_B.stats
        ├── 2612_ERR5766176.stats
        ├── 2613_ERR5766181.stats
        └── ERR3201952_ERR3201952.stats

PR checklist

github-actions · 2026-03-01T13:51:49Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/taxprofiler master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/taxprofiler dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2026-03-01T13:54:39Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 80f0f62

+| ✅ 314 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  18 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-taxprofiler_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-taxprofiler_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowTaxprofiler.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.2.7dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.preprocessing_qc_tool= fastqc
nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
nextflow_config - Config default value correct: params.shortread_qc_minlength= 15
nextflow_config - Config default value correct: params.shortread_complexityfilter_tool= bbduk
nextflow_config - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
nextflow_config - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
nextflow_config - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
nextflow_config - Config default value correct: params.longread_adapterremoval_tool= porechop_abi
nextflow_config - Config default value correct: params.longread_filter_tool= nanoq
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minquality= 7
nextflow_config - Config default value correct: params.shortread_redundancyestimation_mode= kmer
nextflow_config - Config default value correct: params.diamond_output_format= tsv
nextflow_config - Config default value correct: params.kaiju_taxon_rank= species
nextflow_config - Config default value correct: params.krakenuniq_batch_size= 20
nextflow_config - Config default value correct: params.malt_mode= BlastN
nextflow_config - Config default value correct: params.motus_longprep_splittinglength= 300
nextflow_config - Config default value correct: params.motus_longprep_minlen= 50
nextflow_config - Config default value correct: params.ganon_report_type= reads
nextflow_config - Config default value correct: params.ganon_report_rank= default
nextflow_config - Config default value correct: params.ganon_report_toppercentile= 0
nextflow_config - Config default value correct: params.ganon_report_mincount= 0
nextflow_config - Config default value correct: params.ganon_report_maxcount= 0
nextflow_config - Config default value correct: params.sylph_data_type= relative_abundance
nextflow_config - Config default value correct: params.standardisation_taxpasta_format= tsv
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_falcobbduk.nf.test' contains outdir parameter
nf_test_content - 'tests/test_falcobbduk.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_falcobbduk.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_falcobbduk.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/minimal.nf.test' contains outdir parameter
nf_test_content - 'tests/minimal.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/minimal.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/minimal.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_fastpnonpareilkrakenuniq.nf.test' contains outdir parameter
nf_test_content - 'tests/test_fastpnonpareilkrakenuniq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_fastpnonpareilkrakenuniq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_fastpnonpareilkrakenuniq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_alternativepreprocessing.nf.test' contains outdir parameter
nf_test_content - 'tests/test_alternativepreprocessing.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_alternativepreprocessing.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_alternativepreprocessing.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.04.2, Config: 25.04.2
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: labeler.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - BRACKEN_BRACKEN found in conf/base.config and Nextflow scripts.
base_config - SYLPHTAX_TAXPROF found in conf/base.config and Nextflow scripts.
base_config - CENTRIFUGE_KREPORT found in conf/base.config and Nextflow scripts.
base_config - KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE found in conf/base.config and Nextflow scripts.
base_config - MEGAN_RMA2INFO_TSV found in conf/base.config and Nextflow scripts.
base_config - MEGAN_RMA2INFO_KRONA found in conf/base.config and Nextflow scripts.
base_config - FALCO found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - FALCO found in conf/modules.config and Nextflow scripts.
modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_NONPAREIL found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_CURVE found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_SET found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_NONPAREILCURVESR found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - PORECHOP_PORECHOP found in conf/modules.config and Nextflow scripts.
modules_config - PORECHOP_ABI found in conf/modules.config and Nextflow scripts.
modules_config - FILTLONG found in conf/modules.config and Nextflow scripts.
modules_config - NANOQ found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
modules_config - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_RUNS found in conf/modules.config and Nextflow scripts.
modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
modules_config - MEGAN_RMA2INFO_TSV found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_STANDARD_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - BRACKEN_BRACKEN found in conf/modules.config and Nextflow scripts.
modules_config - BRACKEN_COMBINEBRACKENOUTPUTS found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_COMBINEKREPORTS_KRAKEN found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_KREPORT2KRONA found in conf/modules.config and Nextflow scripts.
modules_config - KRONA_CLEANUP found in conf/modules.config and Nextflow scripts.
modules_config - KRONA_KTIMPORTTEXT found in conf/modules.config and Nextflow scripts.
modules_config - MEGAN_RMA2INFO_KRONA found in conf/modules.config and Nextflow scripts.
modules_config - KRONA_KTIMPORTTAXONOMY found in conf/modules.config and Nextflow scripts.
modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
modules_config - METAPHLAN_MERGEMETAPHLANTABLES found in conf/modules.config and Nextflow scripts.
modules_config - CENTRIFUGE_CENTRIFUGE found in conf/modules.config and Nextflow scripts.
modules_config - CENTRIFUGE_KREPORT found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU2TABLE_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU2TABLE_COMBINED found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU2KRONA found in conf/modules.config and Nextflow scripts.
modules_config - DIAMOND_BLASTX found in conf/modules.config and Nextflow scripts.
modules_config - MOTUS_PROFILE found in conf/modules.config and Nextflow scripts.
modules_config - MOTUS_PREPLONG found in conf/modules.config and Nextflow scripts.
modules_config - MOTUS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - KMCP_SEARCH found in conf/modules.config and Nextflow scripts.
modules_config - KMCP_PROFILE found in conf/modules.config and Nextflow scripts.
modules_config - GANON_CLASSIFY found in conf/modules.config and Nextflow scripts.
modules_config - GANON_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - GANON_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - SYLPH_PROFILE found in conf/modules.config and Nextflow scripts.
modules_config - SYLPHTAX_TAXPROF found in conf/modules.config and Nextflow scripts.
modules_config - SYLPHTAX_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - MELON found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-19 09:30:33

jfy133 · 2026-03-01T14:43:10Z

Unstable files to address:

bbduk.log
fastqc.zip
kaiju.tsv
porchop.log

jfy133 · 2026-03-01T14:43:20Z

@nf-core-bot fix linting

…taxprofiler into nftest-alternativepreprocessing

conf/test_alternativepreprocessing.config

tests/test_alternativepreprocessing.nf.test

jfy133 · 2026-03-03T13:51:13Z

@nf-core-bot fix linting

…taxprofiler into nftest-alternativepreprocessing

…plate, use official shortreadfastqpairsonly samplesheet

jfy133 · 2026-03-04T09:30:09Z

@nf-core-bot fix linting

…taxprofiler into nftest-alternativepreprocessing

jfy133 · 2026-03-04T11:28:42Z

@nf-core-bot fix linting

tests/.nftignore

jfy133 · 2026-03-18T10:44:35Z

I'll do a review before I merge that I'm still following the same structure as the two more recent PRs such as #700

jfy133 · 2026-03-19T04:55:13Z

TODO: update config/snapshot to use prinseqplusplus instead for shortread complexity filtering

…lusplus only rtest

sofstam

There is a md5 difference in sylph combined report. This will be adressed in the PR I will open soon

sofstam · 2026-03-19T10:03:53Z

tests/.nftignore

Regarding the inconsistency in the sylph combined report, I would also add the file here, right?

Add basic snapshot

749ecc5

jfy133 requested review from LilyAnderssonLee and sofstam as code owners March 1, 2026 13:51

github-actions bot added the size/m label Mar 1, 2026

jfy133 changed the title ~~Nftest alternativepreprocessing~~ Add nf-test: test_alternativepreprocessing Mar 1, 2026

jfy133 changed the base branch from master to dev March 1, 2026 13:52

jfy133 marked this pull request as draft March 1, 2026 13:52

jfy133 added 2 commits March 1, 2026 15:40

Clean up default test structure

9feafd9

Add first pass snapshot

1e716c9

[automated] Fix code linting

245f98d

github-actions bot added the size/s label Mar 1, 2026

jfy133 added 2 commits March 1, 2026 16:08

Update snapshot

7c2abad

Merge branch 'nftest-alternativepreprocessing' of github.com:nf-core/…

3c30465

…taxprofiler into nftest-alternativepreprocessing

github-actions bot added the size/l label Mar 1, 2026

sofstam reviewed Mar 3, 2026

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jfy133 added 5 commits March 3, 2026 10:56

Standardise variable names suggested by @sofstam

add84e9

Tweak nft-ignore

ece7bd8

Update snapshot

4300f68

Simplify file pickup in getAllFilesFromDir

995530d

Spacing

9e1ab16

nf-core-bot and others added 5 commits March 3, 2026 13:51

[automated] Fix code linting

a83629a

Remove hardcoded ignore file

47c00fc

Merge branch 'nftest-alternativepreprocessing' of github.com:nf-core/…

6584f11

…taxprofiler into nftest-alternativepreprocessing

Implement fix from @maxulysse, reorder .nftignore to better match tem…

dfde919

…plate, use official shortreadfastqpairsonly samplesheet

Finalise snapshot

a11f951

nf-core-bot and others added 3 commits March 4, 2026 09:30

[automated] Fix code linting

75a5fce

Account for porchop variablility

9aa1ca0

Merge branch 'nftest-alternativepreprocessing' of github.com:nf-core/…

60891bf

…taxprofiler into nftest-alternativepreprocessing

jfy133 marked this pull request as ready for review March 4, 2026 11:28

[automated] Fix code linting

2b44588

maxulysse reviewed Mar 4, 2026

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maxulysse approved these changes Mar 4, 2026

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jfy133 requested a review from sofstam March 5, 2026 04:08

jfy133 added 2 commits March 5, 2026 14:40

Merge branch 'dev' into nftest-alternativepreprocessing

7fbeb2b

Fix linting

2565ea8

sofstam approved these changes Mar 18, 2026

View reviewed changes

jfy133 added 3 commits March 18, 2026 11:45

Merge branch 'dev' into nftest-alternativepreprocessing

a05fe01

Merge branch 'dev' into nftest-alternativepreprocessing

e4ba237

Ensure consistency with other profiles

bebfac6

jfy133 marked this pull request as draft March 19, 2026 04:54

jfy133 added 3 commits March 19, 2026 09:53

Merge branch 'dev' into nftest-alternativepreprocessing

3586031

Replace BBDuk to iunstead test prinseqplusplus, removing old prinseqp…

8bde575

…lusplus only rtest

And removal of old config

80f0f62

jfy133 marked this pull request as ready for review March 19, 2026 09:29

jfy133 requested a review from sofstam March 19, 2026 09:30

sofstam approved these changes Mar 19, 2026

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tests/.nftignore

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Regarding the inconsistency in the sylph combined report, I would also add the file here, right?

jfy133 merged commit 9c4734f into dev Mar 19, 2026
16 of 18 checks passed

jfy133 deleted the nftest-alternativepreprocessing branch March 19, 2026 12:10

jfy133 mentioned this pull request Mar 25, 2026

Add nf-test snapshot for all pipeline tests #618

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jfy133 commented Mar 1, 2026

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This PR is against the master branch ❌

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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This PR is against the `master` branch ❌

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️

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