add skeleton summary process

sanger-tol · Dec 12, 2024 · 674b4ad · 674b4ad
1 parent b6f807a
commit 674b4ad
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Showing 5 changed files with 58 additions and 12 deletions.
diff --git a/modules/local/bin_summary/environment.yml b/modules/local/bin_summary/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::r-base=4.4
+  - conda-forge::r-tidyverse=2.0.0
diff --git a/modules/local/bin_summary/main.nf b/modules/local/bin_summary/main.nf
@@ -0,0 +1,17 @@
+process BIN_SUMMARY {
+    label "process_low"
+
+    conda "${moduleDir}/environment.yml"
+    container "docker.io/rocker/tidyverse:4.4"
+
+    input:
+    tuple val(meta), path(stats), path(checkm2), path(taxonomy)
+
+    output:
+    tuple val(meta), path("bin_summary.tsv")
+
+    script:
+    """
+    echo test > bin_summary.tsv
+    """
+}
diff --git a/subworkflows/local/bin_qc.nf b/subworkflows/local/bin_qc.nf
@@ -37,7 +37,7 @@ workflow BIN_QC {
     ch_versions = ch_versions.mix(SEQKIT_STATS.out.versions)
 
     emit:
-    checkm_tsv = ch_checkm2_tsv
-    stats      = SEQKIT_STATS.out.stats
-    versions   = ch_versions
+    checkm2_tsv = ch_checkm2_tsv
+    stats       = SEQKIT_STATS.out.stats
+    versions    = ch_versions
 }
diff --git a/subworkflows/local/binning.nf b/subworkflows/local/binning.nf
@@ -36,7 +36,7 @@ workflow BINNING {
         ch_versions = ch_versions.mix(GAWK_MAXBIN2_DEPTHS.out.versions)
 
         ch_maxbin2_input = assemblies
-            | combine(MAXBIN2_DEPTHS.out.output, by: 0)
+            | combine(GAWK_MAXBIN2_DEPTHS.out.output, by: 0)
             | map { meta, contigs, depths ->
                 [meta, contigs, [], depths]
             }

diff --git a/workflows/longreadmag.nf b/workflows/longreadmag.nf
@@ -14,7 +14,8 @@ include { BINNING                             } from '../subworkflows/local/binn
 include { BIN_QC                              } from '../subworkflows/local/bin_qc.nf'
 include { BIN_TAXONOMY                        } from '../subworkflows/local/bin_taxonomy'
 include { BIN_REFINEMENT                      } from '../subworkflows/local/bin_refinement'
-include { CONTIG2BIN2FASTA as BINS_TO_PROTEIN } from '../modules/local/contig2bin2fasta/main'
+include { BIN_SUMMARY                         } from '../modules/local/bin_summary'
+include { CONTIG2BIN2FASTA as BINS_TO_PROTEIN } from '../modules/local/contig2bin2fasta'
 include { PREPARE_DATA                        } from '../subworkflows/local/prepare_data'
 include { READ_MAPPING                        } from '../subworkflows/local/read_mapping'
 
@@ -113,14 +114,36 @@ workflow LONGREADMAG {
             if(params.enable_binqc) {
                 BIN_QC(ch_bins, ch_aa_bins)
                 ch_versions = ch_versions.mix(BIN_QC.out.versions)
-                ch_checkm2_tsv = BIN_QC.out.checkm_tsv
-            } else {
-                ch_checkm2_tsv = Channel.empty()
-            }
 
-            if(params.enable_taxonomy) {
-                BIN_TAXONOMY(ch_aa_bins, ch_checkm2_tsv)
-                ch_versions = ch_versions.mix(BIN_TAXONOMY.out.versions)
+                if(params.enable_taxonomy) {
+                    BIN_TAXONOMY(ch_aa_bins, BIN_QC.out.checkm2_tsv)
+                    ch_versions = ch_versions.mix(BIN_TAXONOMY.out.versions)
+
+                    ch_taxonomy_tsv = BIN_TAXONOMY.out.gtdb_ncbi
+                } else {
+                    ch_taxonomy_tsv = Channel.empty()
+                }
+
+                if(params.enable_summary) {
+                    ch_stats_collated = BIN_QC.out.stats
+                        | map { meta, stats -> [ meta.subMap('id'), stats] }
+                        | groupTuple(by: 0)
+
+                    ch_checkm2_collated = BIN_QC.out.checkm2_tsv
+                        | map { meta, stats -> [ meta.subMap('id'), stats] }
+                        | groupTuple(by: 0)
+
+                    ch_taxonomy_collated = ch_taxonomy_tsv
+                        | map { meta, stats -> [ meta.subMap('id'), stats] }
+                        | groupTuple(by: 0)
+
+                    ch_bin_summary_input = ch_stats_collated
+                        | combine(ch_checkm2_collated, by: 0)
+                        | combine(ch_taxonomy_collated, by: 0)
+
+                    BIN_SUMMARY(ch_bin_summary_input)
+                    ch_versions = ch_versions.mix(BIN_SUMMARY.out.versions)
+                }
             }
         }
     }