Make binqc_tool an input for BIN_SUMMARY

nf-core · Nov 27, 2024 · ef1828c · ef1828c
1 parent 6152696
commit ef1828c
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Showing 2 changed files with 24 additions and 21 deletions.
diff --git a/modules/local/bin_summary.nf b/modules/local/bin_summary.nf
@@ -1,34 +1,36 @@
 process BIN_SUMMARY {
 
     conda "conda-forge::pandas=1.4.3"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pandas:1.4.3' :
-        'biocontainers/pandas:1.4.3' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
+        : 'biocontainers/pandas:1.4.3'}"
 
     input:
-    path(bin_depths)
-    path(binqc_sum)
-    path(quast_sum)
-    path(gtdbtk_sum)
-    path(cat_sum)
+    path bin_depths
+    path binqc_sum
+    path quast_sum
+    path gtdbtk_sum
+    path cat_sum
+    val  binqc_tool
 
     output:
-    path("bin_summary.tsv"), emit: summary
-    path "versions.yml"    , emit: versions
+    path "bin_summary.tsv", emit: summary
+    path "versions.yml"   , emit: versions
 
     script:
-    def binqc_summary  = binqc_sum.sort().size() > 0 ?  "--binqc_summary ${binqc_sum}" : ""
-    def quast_summary  = quast_sum.sort().size() > 0 ?  "--quast_summary ${quast_sum}" : ""
+    def binqc_summary  = binqc_sum.sort().size() > 0 ? "--binqc_summary ${binqc_sum}" : ""
+    def quast_summary  = quast_sum.sort().size() > 0 ? "--quast_summary ${quast_sum}" : ""
     def gtdbtk_summary = gtdbtk_sum.sort().size() > 0 ? "--gtdbtk_summary ${gtdbtk_sum}" : ""
-    def cat_summary    = cat_sum.sort().size() > 0 ?    "--cat_summary ${cat_sum}" : ""
+    def cat_summary    = cat_sum.sort().size() > 0 ? "--cat_summary ${cat_sum}" : ""
     """
-    combine_tables.py --depths_summary ${bin_depths} \
-                    $binqc_summary \
-                    $quast_summary \
-                    $gtdbtk_summary \
-                    $cat_summary \
-                    --binqc_tool ${params.binqc_tool} \
-                    --out bin_summary.tsv
+    combine_tables.py \
+        --depths_summary ${bin_depths} \
+        ${binqc_summary} \
+        ${quast_summary} \
+        ${gtdbtk_summary} \
+        ${cat_summary} \
+        --binqc_tool ${binqc_tool} \
+        --out bin_summary.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -890,7 +890,8 @@ workflow MAG {
                 ch_bin_qc_summary.ifEmpty([]),
                 ch_quast_bins_summary.ifEmpty([]),
                 ch_gtdbtk_summary.ifEmpty([]),
-                ch_cat_global_summary.ifEmpty([])
+                ch_cat_global_summary.ifEmpty([]),
+                params.binqc_tool
             )
         }