debuging semibin dryrun

metagenome-atlas · Jul 26, 2023 · 2160cda · 2160cda
1 parent 44f1e86
commit 2160cda
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Showing 2 changed files with 15 additions and 8 deletions.
diff --git a/workflow/rules/cobinning.smk b/workflow/rules/cobinning.smk
@@ -61,6 +61,7 @@ def get_bams_of_bingroup(wildcards):
     return expand(
         "Intermediate/cobinning/{bingroup}/bams/{sample}.sorted.bam",
         sample=samples_of_group,
+        bingroup= wildcards.bingroup
     )
 
 

diff --git a/workflow/rules/semibin.smk b/workflow/rules/semibin.smk
@@ -36,7 +36,7 @@ rule semibin_generate_data_multi:
 rule semibin_train:
     input:
         flag="{sample}/{sample}_contigs.fasta",
-        fasta_sample=rules.filter_contigs.output,
+        fasta_sample=rules.filter_contigs.output[0],
         bams=get_bams_of_bingroup,
         data_folder=rules.semibin_generate_data_multi.output[0],
     output:
@@ -74,23 +74,28 @@ rule semibin_train:
 
 def semibin_input(wildcards):
 
-    bingroup_of_sample = sampleTable.loc[wildcards.sample, "bingroup"]
+    bingroup_of_sample = sampleTable.loc[wildcards.sample, "BinGroup"]
     samples_of_bingroup = sampleTable.query(
         f'BinGroup=="{bingroup_of_sample}"'
     ).index.tolist()
 
-    return dict(
-        flag="{sample}/{sample}_contigs.fasta",
-        fasta=rules.filter_contigs.output,
-        bams=lambda wc: expand(rules.sort_bam.output, sample=samples_of_bingroup),
+    assert len(samples_of_bingroup)>1
+
+    mapping= dict(
+        flag=get_assembly(wildcards),
+        fasta=rules.filter_contigs.output[0].format(**wildcards),
+        bams= expand("Intermediate/cobinning/{bingroup}/bams/{sample}.sorted.bam", sample=samples_of_bingroup, bingroup =bingroup_of_sample ),
         data_folder=rules.semibin_generate_data_multi.output[0].format(
-            bingroup=bingroup_of_sample
+            bingroup=bingroup_of_sample,
+            **wildcards
         ),
         model=rules.semibin_train.output[0].format(
-            bingroup=bingroup_of_sample, sample=wildcards.sample
+            bingroup=bingroup_of_sample, **wildcards
         ),
     )
 
+    return mapping
+
 
 rule run_semibin:
     input:
@@ -133,6 +138,7 @@ rule run_semibin:
 localrules:
     parse_semibin_output,
 
+ruleorder: parse_semibin_output > get_unique_cluster_attribution
 
 rule parse_semibin_output:
     input: