From 63a3642832d0b0585bf6ff6d44fdb3462228723c Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 19 Jan 2026 15:08:48 +0100 Subject: [PATCH 1/4] Remove _pe suffix from deliverables --- cg/resources/taxprofiler_bundle_filenames.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cg/resources/taxprofiler_bundle_filenames.yaml b/cg/resources/taxprofiler_bundle_filenames.yaml index 848a8aa242..c6599abba3 100644 --- a/cg/resources/taxprofiler_bundle_filenames.yaml +++ b/cg/resources/taxprofiler_bundle_filenames.yaml @@ -5,12 +5,12 @@ tag: kraken2_combined_report - format: txt id: SAMPLEID - path: PATHTOCASE/kraken2/k2_pluspf/SAMPLENAME_pe_k2_pluspf.kraken2.kraken2.report.txt + path: PATHTOCASE/kraken2/k2_pluspf/SAMPLENAME_k2_pluspf.kraken2.kraken2.report.txt step: kraken2 tag: kraken2_report - format: txt id: SAMPLEID - path: PATHTOCASE/kraken2/k2_pluspf/SAMPLENAME_pe_k2_pluspf.kraken2.kraken2.classifiedreads.txt + path: PATHTOCASE/kraken2/k2_pluspf/SAMPLENAME_k2_pluspf.kraken2.kraken2.classifiedreads.txt step: kraken2 tag: kraken2_classified_reads - format: html @@ -30,7 +30,7 @@ tag: bracken_combined_report - format: tsv id: SAMPLEID - path: PATHTOCASE/bracken/bracken/SAMPLENAME_pe_bracken.bracken.tsv + path: PATHTOCASE/bracken/bracken/SAMPLENAME_bracken.bracken.tsv step: bracken tag: bracken_report - format: txt @@ -40,12 +40,12 @@ tag: centrifuge_combined_report - format: txt id: SAMPLEID - path: PATHTOCASE/centrifuge/p_compressed+h+v/SAMPLENAME_pe_p_compressed+h+v.centrifuge.txt + path: PATHTOCASE/centrifuge/p_compressed+h+v/SAMPLENAME_p_compressed+h+v.centrifuge.txt step: centrifuge tag: centrifuge_report - format: txt id: SAMPLEID - path: PATHTOCASE/centrifuge/p_compressed+h+v/SAMPLENAME_pe_p_compressed+h+v.centrifuge.results.txt + path: PATHTOCASE/centrifuge/p_compressed+h+v/SAMPLENAME_p_compressed+h+v.centrifuge.results.txt step: centrifuge tag: centrifuge_results - format: html From 6aabb65c504777c132953bee3b9b3a3bb3329a82 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 20 Jan 2026 14:23:40 +0100 Subject: [PATCH 2/4] Update path for nf_core_taxprofiler software versions --- cg/resources/taxprofiler_bundle_filenames.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cg/resources/taxprofiler_bundle_filenames.yaml b/cg/resources/taxprofiler_bundle_filenames.yaml index c6599abba3..9363620755 100644 --- a/cg/resources/taxprofiler_bundle_filenames.yaml +++ b/cg/resources/taxprofiler_bundle_filenames.yaml @@ -55,7 +55,7 @@ tag: multiqc-html - format: yml id: CASEID - path: PATHTOCASE/pipeline_info/nf_core_pipeline_software_mqc_versions.yml + path: PATHTOCASE/pipeline_info/nf_core_taxprofiler_software_mqc_versions.yml step: software-versions tag: software-versions - format: json From b33853108f6f89916919a0e064ab72bf821caf73 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 20 Jan 2026 14:44:01 +0100 Subject: [PATCH 3/4] Remove multiqc_general_stats --- cg/resources/taxprofiler_bundle_filenames.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/cg/resources/taxprofiler_bundle_filenames.yaml b/cg/resources/taxprofiler_bundle_filenames.yaml index 9363620755..71c4a15b75 100644 --- a/cg/resources/taxprofiler_bundle_filenames.yaml +++ b/cg/resources/taxprofiler_bundle_filenames.yaml @@ -68,11 +68,6 @@ path: PATHTOCASE/CASEID_metrics_deliverables.yaml step: qc-metrics tag: qc-metrics -- format: json - id: CASEID - path: PATHTOCASE/multiqc/multiqc_data/multiqc_general_stats.json - step: multiqc-json - tag: multiqc-general-stats - format: json id: CASEID path: PATHTOCASE/multiqc/multiqc_data/multiqc_fastp.json From 8c91a953be978e5524b6c3b0488925981d86d454 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 20 Jan 2026 15:08:06 +0100 Subject: [PATCH 4/4] Remove multiqc JSON file entries from YAML --- cg/resources/taxprofiler_bundle_filenames.yaml | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/cg/resources/taxprofiler_bundle_filenames.yaml b/cg/resources/taxprofiler_bundle_filenames.yaml index 71c4a15b75..5a1a852159 100644 --- a/cg/resources/taxprofiler_bundle_filenames.yaml +++ b/cg/resources/taxprofiler_bundle_filenames.yaml @@ -68,21 +68,6 @@ path: PATHTOCASE/CASEID_metrics_deliverables.yaml step: qc-metrics tag: qc-metrics -- format: json - id: CASEID - path: PATHTOCASE/multiqc/multiqc_data/multiqc_fastp.json - step: multiqc-json - tag: multiqc-fastp -- format: json - id: CASEID - path: PATHTOCASE/multiqc/multiqc_data/multiqc_samtools_stats.json - step: multiqc-json - tag: multiqc-samtools-stats -- format: json - id: CASEID - path: PATHTOCASE/multiqc/multiqc_data/multiqc_kraken.json - step: multiqc-json - tag: multiqc-kraken - format: json id: CASEID path: PATHTOCASE/manifest.json