Merge pull request #676 from d4straub/fix_phyloseq_input

Fix phyloseq input
nf-core · Dec 12, 2023 · 746c524 · 746c524
2 parents 0b29755 + 99b1db6
commit 746c524
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Showing 5 changed files with 7 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#672](https://github.com/nf-core/ampliseq/pull/672) - Update output docs for collapsed abundance tables
 - [#673](https://github.com/nf-core/ampliseq/pull/673) - Fix logic relating to generation of qiime2 taxonomy part of summary report
+- [#676](https://github.com/nf-core/ampliseq/pull/676) - Phyloseq sometimes only produced one of multiple output files
 
 ### `Dependencies`
 

diff --git a/modules/local/phyloseq.nf b/modules/local/phyloseq.nf
@@ -8,8 +8,7 @@ process PHYLOSEQ {
         'biocontainers/bioconductor-phyloseq:1.44.0--r43hdfd78af_0' }"
 
     input:
-    tuple val(prefix), path(tax_tsv)
-    path otu_tsv
+    tuple val(prefix), path(tax_tsv), path(otu_tsv)
     path sam_tsv
     path tree
 

diff --git a/subworkflows/local/phyloseq_workflow.nf b/subworkflows/local/phyloseq_workflow.nf
@@ -36,7 +36,7 @@ workflow PHYLOSEQ_WORKFLOW {
         ch_phyloseq_inasv = ch_tsv
     }
 
-    PHYLOSEQ ( ch_tax, ch_phyloseq_inasv, ch_phyloseq_inmeta, ch_phyloseq_intree )
+    PHYLOSEQ ( ch_tax.combine(ch_phyloseq_inasv), ch_phyloseq_inmeta, ch_phyloseq_intree )
 
     emit:
     rds     = PHYLOSEQ.out.rds

diff --git a/tests/pipeline/pplace.nf.test b/tests/pipeline/pplace.nf.test
@@ -57,7 +57,8 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/qiime2_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/qiime2_phyloseq.rds").exists() },
+                { assert new File("$outputDir/phyloseq/pplace_phyloseq.rds").exists() }
             )
         }
     }

diff --git a/tests/pipeline/reftaxcustom.nf.test b/tests/pipeline/reftaxcustom.nf.test
@@ -48,7 +48,8 @@ nextflow_pipeline {
                                 path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
                 { assert new File("$outputDir/summary_report/summary_report.html").exists() },
-                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() }
+                { assert new File("$outputDir/phyloseq/dada2_phyloseq.rds").exists() },
+                { assert new File("$outputDir/phyloseq/kraken2_phyloseq.rds").exists() }
             )
         }
     }