--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/bcs_results/main.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,43 @@
+process BCS_RESULTS {
+    tag "bettercallsal aggregate"
+    label "process_pico"
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+
+    input:
+        path salmon_res_dirs
+
+    output:
+        path 'bettercallsal*.tblsum.txt', emit: mqc_txt, optional: true
+        path 'bettercallsal*_mqc.json'  , emit: mqc_json, optional: true
+        path 'bettercallsal*_mqc.yml'   , emit: mqc_yml, optional: true
+        path 'versions.yml'             , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        args += (params.tuspy_ps ? " -pickle ${params.tuspy_ps}" : '')
+        args += (params.gsrpy_snp_clus_metadata ? " -snp ${params.gsrpy_snp_clus_metadata}" : '')
+        """
+        gen_salmon_res_table.py \\
+            $args \\
+            -sal "."
+
+        create_mqc_data_table.py \\
+            "bettercallsal" "The following table is an aggregation of serotype calls from all samples which also includes read counts from <code>salmon quant</code> results."
+
+        create_mqc_data_table.py \\
+            "bettercallsal_salyn" "The following table summarizes serotype presence or absence for all samples."
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            python: \$( python --version | sed 's/Python //g' )
+        END_VERSIONS
+        """
+}
\ No newline at end of file