merge dev to the current branch

nf-core · Sep 5, 2024 · 75efdb7 · 75efdb7
2 parents 8a42385 + 5e0d556
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#518](https://github.com/nf-core/taxprofiler/pull/518) Fixed a bug where Oxford Nanopore FASTA input files would not be processed (❤️ to @ikarls for reporting, fixed by @jfy133)
+
 ### `Dependencies`
 
 | Tool      | Previous version | New version |

diff --git a/docs/usage.md b/docs/usage.md
@@ -97,6 +97,10 @@ While one can include both short-read and long-read data in one run, we recommen
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
+:::warning
+FASTA input will not go through any preprocessing steps, and will go directly to profiling.
+:::
+
 ### Full database sheet
 
 nf-core/taxprofiler supports multiple databases being classified/profiled against in parallel for each tool.

diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
@@ -136,7 +136,7 @@ workflow TAXPROFILER {
         .branch { meta, run_accession, instrument_platform, fastq_1, fastq_2, fasta ->
             fastq: meta.single_end || fastq_2
                 return [ meta + [ type: "short" ], fastq_2 ? [ fastq_1, fastq_2 ] : [ fastq_1 ] ]
-            nanopore: instrument_platform == 'OXFORD_NANOPORE'
+            nanopore: instrument_platform == 'OXFORD_NANOPORE' && !meta.is_fasta
                 meta.single_end = true
                 return [ meta + [ type: "long" ], [ fastq_1 ] ]
             fasta: meta.is_fasta
@@ -145,7 +145,7 @@ workflow TAXPROFILER {
         }
 
     // Merge ch_input.fastq and ch_input.nanopore into a single channel
-    def ch_input_for_fastqc = ch_input.fastq.mix( ch_input.nanopore )
+    ch_input_for_fastqc = ch_input.fastq.mix( ch_input.nanopore )
 
     // Validate and decompress databases
     ch_dbs_for_untar = databases