--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/nowayout_results/main.nf	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,45 @@
+process NOWAYOUT_RESULTS {
+    tag "nowayout aggregate"
+    label "process_pico"
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
+    conda (params.enable_conda ? 'conda-forge::python=3.11 conda-forge::spectra conda-forge::lzstring conda-forge::imp bioconda::multiqc=1.19' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0' }"
+
+    input:
+        path pass_and_fail_rel_abn_files
+        path lineage_csv
+
+    output:
+        path '*.tblsum.txt', emit: mqc_txt, optional: true
+        path '*_mqc.json'  , emit: mqc_json, optional: true
+        path '*_mqc.yml'   , emit: mqc_yml, optional: true
+        path '*.tsv'       , emit: tsv, optional: true
+        path 'versions.yml', emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        """
+        gen_salmon_tph_and_krona_tsv.py \\
+            $args \\
+            -sal "." \\
+            -smres "." \\
+            -lin $lineage_csv
+
+        create_mqc_data_table.py \\
+            "nowayout" "The results shown here are <code>salmon quant</code> TPM values scaled down by a factor of ${params.gsalkronapy_sf}."
+
+        create_mqc_data_table.py \\
+            "nowayout_indiv_reads_mapped" "The results shown here are the number of reads mapped (post threshold filters) per taxon to the <code>nowayout</code>'s custom <code>${params.db_mode}</code> database for each sample."
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            python: \$( python --version | sed 's/Python //g' )
+        END_VERSIONS
+        """
+}
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