Snapshot for -profile test_single_end

CHANGELOG.md

@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#905](https://github.com/nf-core/mag/pull/905) - Add nf-test snapshot for `test_assembly_input` profile (by @dialvarezs)
+- [#908](https://github.com/nf-core/mag/pull/908) - Add nf-test snapshot for `test_single_end` profile (by @dialvarezs)
 - [#930](https://github.com/nf-core/mag/pull/930) - Add binner SemiBin2 (by @d4straub)
 
 ### `Changed`
@@ -37,6 +38,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
+- [#908](https://github.com/nf-core/mag/pull/908) - Removed local `quast_bins_summary` in favor of `csvtk/concat` (by @dialvarezs)
+
 ## v5.2.0 - Puce Pangolin [2025-11-07]
 
 ### `Added`

bin/summary_gtdbtk.py

@@ -63,12 +63,7 @@ def parse_args(args=None):
 def main(args=None):
     args = parse_args(args)
 
-    if (
-        not args.summaries
-        and not args.filtered_bins
-        and not args.failed_bins
-        and not args.qc_discarded_bins
-    ):
+    if not args.summaries and not args.filtered_bins and not args.failed_bins and not args.qc_discarded_bins:
         sys.exit(
             "Either --summaries, --filtered_bins, --failed_bins or --qc_discarded_bins must be specified!"
         )
@@ -133,9 +128,7 @@ def main(args=None):
         for file in args.summaries:
             df_summary = pd.read_csv(file, sep="\t")[columns]
             # add by GTDB-Tk substracted file extension again to bin names (at least until changed consistently in rest of pipeline)
-            df_summary["user_genome"] = (
-                df_summary["user_genome"].astype(str) + "." + args.extension
-            )
+            df_summary["user_genome"] = df_summary["user_genome"].astype(str) + "." + args.extension
             df_summary.set_index("user_genome", inplace=True)
             df_final = df_final.append(df_summary, verify_integrity=True)
 
@@ -171,9 +164,7 @@ def main(args=None):
                 filtered.append(bin_results)
 
     df_filtered = pd.DataFrame(filtered, columns=columns)
-    df_filtered["user_genome"] = (
-        df_filtered["user_genome"].astype(str) + "." + args.extension
-    )
+    df_filtered["user_genome"] = df_filtered["user_genome"].astype(str) + "." + args.extension
     df_filtered.set_index("user_genome", inplace=True)
     df_final = df_final.append(df_filtered, verify_integrity=True)
 
@@ -209,14 +200,12 @@ def main(args=None):
                 failed.append(bin_results)
 
     df_failed = pd.DataFrame(failed, columns=columns)
-    df_failed["user_genome"] = (
-        df_failed["user_genome"].astype(str) + "." + args.extension
-    )
+    df_failed["user_genome"] = df_failed["user_genome"].astype(str) + "." + args.extension
     df_failed.set_index("user_genome", inplace=True)
     df_final = df_final.append(df_failed, verify_integrity=True)
 
     # write output
-    df_final.reset_index().rename(columns={"index": "user_genome"}).to_csv(
+    df_final.reset_index().rename(columns={"index": "user_genome"}).sort_values("user_genome").to_csv(
         args.out, sep="\t", index=False
     )
 

conf/modules.config

@@ -407,7 +407,7 @@ process {
         publishDir = [path: { "${params.outdir}/Assembly/${meta.assembler}/QC/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
     }
 
-    withName: 'QUAST_BINS|QUAST_BINS_SUMMARY' {
+    withName: 'QUAST_BINS|CONCAT_QUAST_SUMMARY' {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC" },
             mode: params.publish_dir_mode,
@@ -715,6 +715,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -724,6 +725,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 

docs/output.md

@@ -577,7 +577,7 @@ For each bin or refined bin the median sequencing depth is computed based on the
   - `predicted_genes/barrnap.log`: Barrnap log file (ribosomal RNA predictor)
 - `GenomeBinning/QC/`
   - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]-quast_summary.tsv`: QUAST output summarized per sample/condition.
-  - `quast_summary.tsv`: QUAST output for all bins summarized
+  - `quast_bin_summary.tsv`: QUAST output for all bins summarized
 
 </details>
 

subworkflows/local/bin_qc/main.nf

@@ -132,6 +132,9 @@ workflow BIN_QC {
             .filter { meta, _bins ->
                 meta.domain != "eukarya"
             }
+            .map { meta, bins ->
+                [meta, bins.sort { a, b -> a.getBaseName() <=> b.getBaseName() }]
+            }
             .multiMap { meta, fa ->
                 reads: [meta, fa]
                 ext: fa.extension.unique().join("")
@@ -152,6 +155,9 @@ workflow BIN_QC {
         ch_checkm_summaries = CHECKM_QA.out.output
             .map { _meta, summary -> [[id: 'checkm'], summary] }
             .groupTuple()
+            .map { meta, summaries ->
+                [meta, summaries.sort { a, b -> a.getBaseName() <=> b.getBaseName() }]
+            }
         ch_multiqc_files = ch_multiqc_files.mix(
             CHECKM_QA.out.output.map { _meta, summary -> summary }.flatten()
         )

subworkflows/local/binning/main.nf

@@ -162,7 +162,7 @@ workflow BINNING {
     // SemiBin2
     if (!params.skip_semibin) {
         ch_semibin_input = ch_assemblies
-            .map { meta, assembly, bams, bais ->
+            .map { meta, assembly, bams, _bais ->
                 def meta_new = meta + [binner: 'SemiBin2']  + [sample_count: bams.size()]
                 [meta_new, assembly, bams]
             }

subworkflows/local/catpack/main.nf

@@ -86,6 +86,7 @@ workflow CATPACK {
             name: 'bat_summary.tsv',
             storeDir: "${params.outdir}/Taxonomy/CAT/",
             keepHeader: true,
+            sort: 'deep',
         )
 
     if (!params.cat_allow_unofficial_lineages) {

tests/.nftignore

@@ -1,6 +1,12 @@
 .DS_Store
+Ancient_DNA/pydamage/analyze/*/*.csv
+Ancient_DNA/variant_calling/*/*.vcf.gz
+Annotation/Prokka/**/*.{log,err,gbk,sqn}
+Annotation/Prokka/**/*.tmp.*
 Assembly/MEGAHIT/*.log
 Assembly/MEGAHIT/QC/*/*.bowtie2.log
+Assembly/MEGAHIT/QC/*/QUAST/*.{pdf,html,log}
+Assembly/MEGAHIT/QC/*/QUAST/**/*.{pdf,html}
 GenomeBinning/CONCOCT/stats/*_{original,PCA_components,PCA_transformed}_data_gt1000.csv
 GenomeBinning/CONCOCT/stats/*_log.txt
 GenomeBinning/CONCOCT/stats/*.tsv
@@ -17,8 +23,13 @@ GenomeBinning/QC/BUSCO/**/*.log
 GenomeBinning/QC/BUSCO/**/*.txt
 GenomeBinning/QC/BUSCO/**/short_summary*.{txt,json}
 GenomeBinning/QC/BUSCO/*/*{-busco.log,-busco.batch_summary.txt}
+GenomeBinning/QC/CheckM/*/{checkm.log,lineage.ms}
+GenomeBinning/QC/CheckM/*/bins/*/hmmer.{analyze,tree}.txt
+GenomeBinning/QC/CheckM/*/storage/*
 GenomeBinning/QC/CheckM2/**/DIAMOND_RESULTS.tsv
 GenomeBinning/QC/CheckM2/*/checkm2.log
+GenomeBinning/QC/QUAST/*/*.{pdf,html,log}
+GenomeBinning/QC/QUAST/*/**/*.{pdf,html}
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
 multiqc/multiqc_data/llms-full.txt
 multiqc/multiqc_data/multiqc_data.json
@@ -33,3 +44,5 @@ multiqc/multiqc_report.html
 pipeline_info/*.{html,json,txt,yml}
 QC_shortreads/fastqc/*_fastqc.{html,zip}
 QC_shortreads/remove_phix/*.log
+Taxonomy/CAT/**/*.log
+VirusIdentification/geNomad/**/*_aggregated_classification.tsv

tests/default.nf.test.snap

@@ -47,6 +47,9 @@
                 "CONCAT_BUSCO_TSV": {
                     "csvtk": "0.31.0"
                 },
+                "CONCAT_QUAST_SUMMARY": {
+                    "csvtk": "0.31.0"
+                },
                 "CONVERT_DEPTHS": {
                     "bioawk": 20110810
                 },
@@ -122,9 +125,6 @@
                     "metaquast": "5.0.2",
                     "python": "3.7.6"
                 },
-                "QUAST_BINS_SUMMARY": {
-                    "cp": 9.5
-                },
                 "SEMIBIN_SINGLEEASYBIN": {
                     "SemiBin": "2.2.0"
                 },

tests/test_assembly_input.nf.test

@@ -89,10 +89,10 @@ nextflow_pipeline {
                     workflow.trace.succeeded().size(),
                     removeNextflowVersion("${outputDir}/pipeline_info/nf_core_mag_software_mqc_versions.yml"),
                 ).match() },
-                { assert snapshot(stable_name_assembly).match('assembly') },
+                { assert snapshot(stable_name_assembly                          ).match('assembly') },
                 { assert snapshot(stable_name_annotation, stable_path_annotation).match('annotation') },
-                { assert snapshot(stable_name_binning,  stable_path_binning ).match('binning') },
-                { assert snapshot(stable_name_multiqc, stable_path_multiqc).match('multiqc') },
+                { assert snapshot(stable_name_binning,    stable_path_binning   ).match('binning') },
+                { assert snapshot(stable_name_multiqc,    stable_path_multiqc   ).match('multiqc') },
 
                 // FASTA checks
                 { assert concoct_bins.collect { file -> path("${file}").fasta.size() > 0 }.every() },

tests/test_hybrid.nf.test.snap

@@ -42,6 +42,9 @@
                 "CONCAT_BUSCO_TSV": {
                     "csvtk": "0.31.0"
                 },
+                "CONCAT_QUAST_SUMMARY": {
+                    "csvtk": "0.31.0"
+                },
                 "CONVERT_DEPTHS": {
                     "bioawk": 20110810
                 },
@@ -114,9 +117,6 @@
                     "metaquast": "5.0.2",
                     "python": "3.7.6"
                 },
-                "QUAST_BINS_SUMMARY": {
-                    "cp": 9.5
-                },
                 "SAMTOOLS_HOSTREMOVED_INDEX": {
                     "samtools": "1.22.1"
                 },

tests/test_longreadonly.nf.test.snap

@@ -19,6 +19,9 @@
                 "CONCAT_BUSCO_TSV": {
                     "csvtk": "0.31.0"
                 },
+                "CONCAT_QUAST_SUMMARY": {
+                    "csvtk": "0.31.0"
+                },
                 "CONVERT_DEPTHS": {
                     "bioawk": 20110810
                 },
@@ -95,9 +98,6 @@
                     "metaquast": "5.0.2",
                     "python": "3.7.6"
                 },
-                "QUAST_BINS_SUMMARY": {
-                    "cp": 9.5
-                },
                 "SAMTOOLS_HOSTREMOVED_INDEX": {
                     "samtools": "1.22.1"
                 },