dryrun passed

metagenome-atlas · Jul 26, 2023 · 25bebfb · 25bebfb
1 parent d96386b
commit 25bebfb
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Showing 2 changed files with 11 additions and 6 deletions.
diff --git a/workflow/rules/cobinning.smk b/workflow/rules/cobinning.smk
@@ -52,6 +52,11 @@ def get_filtered_contigs_of_bingroup(wildcards):
     }
 
 
+def get_bams_of_bingroup(wildcards):
+
+    samples_of_group = get_samples_of_bingroup(wildcards)
+
+    return expand("Intermediate/cobinning/{bingroup}/bams/{sample}.sorted.bam", sample= samples_of_group)
 
 
 rule combine_contigs:
@@ -161,7 +166,7 @@ rule sort_bam:
 
 rule summarize_bam_contig_depths:
     input:
-        bam=expand(rules.sort_bam.output, sample=SAMPLES),
+        bams= get_bams_of_bingroup,
     output:
         "Intermediate/cobinning/{bingroup}/coverage.jgi.tsv",
     log:
@@ -174,7 +179,7 @@ rule summarize_bam_contig_depths:
     shell:
         "jgi_summarize_bam_contig_depths "
         " --outputDepth {output} "
-        " {input.bam} &> {log} "
+        " {input.bams} &> {log} "
 
 
 localrules:
@@ -233,7 +238,7 @@ localrules:
 
 rule parse_vamb_output:
     input:
-        expand(rules.run_vamb.output, bingroup = SampleTable.BinGroup.unique()),
+        expand(rules.run_vamb.output, bingroup = sampleTable.BinGroup.unique()),
     output:
         renamed_clusters="Intermediate/cobinning/vamb_clusters.tsv.gz",
         cluster_atributions= expand(vamb_cluster_attribution_path, sample=SAMPLES),

diff --git a/workflow/rules/semibin.smk b/workflow/rules/semibin.smk
@@ -2,7 +2,7 @@
 rule semibin_generate_data_multi:
     input:
         fasta=rules.combine_contigs.output,
-        bams=lambda wc: expand(rules.sort_bam.output, sample= get_samples_of_bingroup(wc)),
+        bams=get_bams_of_bingroup,
     output:
         directory("Intermediate/cobinning/{bingroup}/semibin/data_multi")
         # expand(
@@ -37,7 +37,7 @@ rule semibin_train:
     input:
         flag = "{sample}/{sample}_contigs.fasta",
         fasta_sample = rules.filter_contigs.output,
-        bams= rules.semibin_generate_data_multi.input.bams,
+        bams= get_bams_of_bingroup,
         data_folder= rules.semibin_generate_data_multi.output[0],
     output:
         "Intermediate/cobinning/{bingroup}/semibin/models/{sample}/model.h5",
@@ -97,7 +97,7 @@ rule run_semibin:
     benchmark:
         "logs/benchmarks/semibin/bin/{sample}.tsv"
     params:
-        output_dir= lambda wc, output: os.path.dirname(output[0])
+        output_dir= lambda wc, output: os.path.dirname(output[0]),
         data = lambda wc, input: Path(input.data_folder)/"samples"/wc.sample/"data.csv",
         min_bin_kbs=int(config["cobining_min_bin_size"] / 1000),
         extra=config["semibin_options"],