updated summary of bins

cwl/workflows/workflow_metagenomics_binning.cwl

@@ -46,6 +46,11 @@ outputs:
     doc: GTDB-Tk output directory
     type: Directory?
     outputSource: gtdbtk_files_to_folder/results
+  bins_summary:
+    label: Bins summary
+    doc: Summary of info about the bins
+    type: File
+    outputSource: bins_summary/bins_summary
 
 inputs:
   identifier:
@@ -150,14 +155,17 @@ steps:
     out: [binDepths]
 #############################################
 #### Bin assembly statistics
-  bins_stats:
-    doc: Table of all bins and their assembly statistics like N50
-    label: Bin assembly stats
-    run: ../metagenomics/bin_assembly_stats.cwl
+  bins_summary:
+    doc: Table of all bins and their statistics like size, contigs, completeness etc
+    label: Bins summary
+    run: ../metagenomics/bins_summary.cwl
     in:
       identifier: identifier
       bin_dir: metabat2/bin_dir
-    out: [binStats,binContigs]
+      busco_dir: busco_files_to_folder/results 
+      bin_depths: aggregate_bin_depths/binDepths
+      checkm: checkm/checkm_out_table
+    out: [bins_summary, bin_contigs]
 #############################################
 #### Get unbinned contigs fasta
   # workflow_getunbinned:
@@ -170,15 +178,15 @@ steps:
   #     assembly_fasta: assembly
   #     bin_dir: workflow_metabat2/bin_dir
   #   out: [unbinned_fasta]
-#############################################
-#### General bin and assembly read mapping stats
+############################################
+### General bin and assembly read mapping stats
   bin_readstats:
     doc: Table general bin and assembly read mapping stats
     label: Bin and assembly read stats
     run: ../metagenomics/assembly_bins_readstats.cwl
     in:
       identifier: identifier
-      binContigs: bins_stats/binContigs
+      binContigs: bins_summary/bin_contigs
       idxstats: contig_read_counts/contigReadCounts
       flagstat: assembly_read_counts/flagstat
     out: [binReadStats]
@@ -275,8 +283,8 @@ steps:
     label: MetaBat2 output folder
     run: ../expressions/files_to_folder.cwl
     in:
-      files: 
-        source: [metabat2/log, bins_stats/binStats, bin_readstats/binReadStats, bins_stats/binContigs, metabat2_contig_depths/depths, aggregate_bin_depths/binDepths]
+      files:
+        source: [metabat2/log, bins_summary/bin_contigs ,bin_readstats/binReadStats, metabat2_contig_depths/depths, aggregate_bin_depths/binDepths]
         linkMerge: merge_flattened
       folders:
         source: [metabat2/bin_dir]