From 7f82975e6dcba2135632adaaee3afe8795c6fd83 Mon Sep 17 00:00:00 2001
From: LilyAnderssonLee <lilili2011me@gmail.com>
Date: Thu, 21 Mar 2024 12:48:31 +0100
Subject: [PATCH] update nf-validation and turn off kaiju2krona output

---
 .github/workflows/download_pipeline.yml | 12 +++++++++-
 conf/modules.config                     |  4 ++++
 workflows/taxprofiler.nf                | 32 ++++++++++++-------------
 3 files changed, 30 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 08622fd5..2560d9c4 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -65,8 +65,18 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results{% endraw %}
diff --git a/conf/modules.config b/conf/modules.config
index 6fb846b4..e3fb0f18 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -633,6 +633,10 @@ process {
     withName: KAIJU_KAIJU2KRONA {
         tag = {"${meta.db_name}|${meta.id}"}
         ext.args = '-v -u'
+        publishDir = [
+            path: { "${params.outdir}/kaiju/" },
+            enabled : false
+        ]
     }
 
     withName: DIAMOND_BLASTX {
diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf
index ccee03f3..cc6955cf 100644
--- a/workflows/taxprofiler.nf
+++ b/workflows/taxprofiler.nf
@@ -110,8 +110,8 @@ workflow TAXPROFILER {
     ch_multiqc_files = Channel.empty()
 
     // Validate input files and create separate channels for FASTQ, FASTA, and Nanopore data
-    samplesheet
-        .branch { meta, run_accession, instrument_platform, fastq_1, fastq_2, fasta ->
+    ch_input = samplesheet
+        .map { meta, run_accession, instrument_platform, fastq_1, fastq_2, fasta ->
             meta.run_accession = run_accession
             meta.instrument_platform = instrument_platform
 
@@ -130,23 +130,21 @@ workflow TAXPROFILER {
             if ( meta.single_end && fastq_2 ) {
                 error("Error: Please check input samplesheet: for single-end reads entry `fastq_2` should be empty")
             }
-            fastq_se: meta.single_end
-                return [ meta, [ fastq_1 ] ]
+            return [ meta, run_accession, instrument_platform, fastq_1, fastq_2, fasta ]
+        }
+        .branch { meta, run_accession, instrument_platform, fastq_1, fastq_2, fasta ->
+            fastq: meta.single_end || fastq_2
+                return [ meta, fastq_2 ? [ fastq_1, fastq_2 ] : [ fastq_1 ] ]
             nanopore: instrument_platform == 'OXFORD_NANOPORE'
                 meta.single_end = true
                 return [ meta, [ fastq_1 ] ]
-            fastq_pe: fastq_2
-                return [ meta, [ fastq_1, fastq_2 ] ]
-            ch_fasta: meta.is_fasta
+            fasta: meta.is_fasta
                 meta.single_end = true
-                return [ meta, [fasta] ]
+                return [ meta, [ fasta ] ]
         }
-        .set { ch_input }
 
-    // Merge ch_input.fastq_pe and ch_input.fastq_se into a single channel
-    def ch_fastq = ch_input.fastq_pe.mix( ch_input.fastq_se )
-    // Merge ch_fastq and ch_input.nanopore into a single channel
-    def ch_input_for_fastqc = ch_fastq.mix( ch_input.nanopore )
+    // Merge ch_input.fastq and ch_input.nanopore into a single channel
+    def ch_input_for_fastqc = ch_input.fastq.mix( ch_input.nanopore )
 
     // Validate and decompress databases
     ch_dbs_for_untar = databases
@@ -190,10 +188,10 @@ workflow TAXPROFILER {
     */
 
     if ( params.perform_shortread_qc ) {
-        ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( ch_fastq, adapterlist ).reads
+        ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( ch_input.fastq, adapterlist ).reads
         ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
     } else {
-        ch_shortreads_preprocessed = ch_fastq
+        ch_shortreads_preprocessed = ch_input.fastq
     }
 
     if ( params.perform_longread_qc ) {
@@ -262,13 +260,13 @@ workflow TAXPROFILER {
                 meta, reads ->
                 [ meta, [ reads ].flatten() ]
             }
-            .mix( ch_input.ch_fasta )
+            .mix( ch_input.fasta )
 
         ch_versions = ch_versions.mix(MERGE_RUNS.out.versions)
 
     } else {
         ch_reads_runmerged = ch_shortreads_hostremoved
-            .mix( ch_longreads_hostremoved, ch_input.ch_fasta )
+            .mix( ch_longreads_hostremoved, ch_input.fasta )
     }
 
     /*