use function get_assembly

metagenome-atlas · Jul 26, 2023 · e7d3b3e · e7d3b3e
1 parent 8062f18
commit e7d3b3e
Show file tree

Hide file tree

Showing 5 changed files with 27 additions and 16 deletions.
diff --git a/workflow/rules/assemble.smk b/workflow/rules/assemble.smk
@@ -608,7 +608,7 @@ rule finalize_contigs:
 
 rule calculate_contigs_stats:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
     output:
         "{sample}/assembly/contig_stats/final_contig_stats.txt",
     conda:
@@ -648,7 +648,7 @@ rule align_reads_to_final_contigs:
 
 rule pileup_contigs_sample:
     input:
-        fasta="{sample}/{sample}_contigs.fasta",
+        fasta=get_assembly,
         bam="{sample}/sequence_alignment/{sample}.bam",
     output:
         covhist="{sample}/assembly/contig_stats/postfilter_coverage_histogram.txt",
@@ -702,7 +702,7 @@ rule create_bam_index:
 
 rule predict_genes:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
     output:
         fna="{sample}/annotation/predicted_genes/{sample}.fna",
         faa="{sample}/annotation/predicted_genes/{sample}.faa",

diff --git a/workflow/rules/binning.smk b/workflow/rules/binning.smk
@@ -1,14 +1,12 @@
 from glob import glob
 
-BINNING_CONTIGS = "{sample}/{sample}_contigs.fasta"
-
 
 include: "bin_quality.smk"
 
 
 rule pileup_for_binning:
     input:
-        fasta=BINNING_CONTIGS,
+        fasta=get_assembly,
         bam="{sample}/sequence_alignment/{sample_reads}.bam",
     output:
         covstats="{sample}/binning/coverage/{sample_reads}_coverage_stats.txt",
@@ -79,7 +77,7 @@ rule combine_coverages:
 rule run_concoct:
     input:
         coverage="{sample}/binning/coverage/combined_coverage.tsv",
-        fasta=BINNING_CONTIGS,
+        fasta=get_assembly,
     output:
         "{{sample}}/binning/concoct/intermediate_files/clustering_gt{}.csv".format(
             config["concoct"]["min_contig_length"]
@@ -159,7 +157,7 @@ def get_metabat_sensitivity():
 rule metabat:
     input:
         depth_file=rules.get_metabat_depth_file.output,
-        contigs=BINNING_CONTIGS,
+        contigs=get_assembly,
     output:
         "{sample}/binning/metabat/cluster_attribution.tmp",
     params:
@@ -190,7 +188,7 @@ rule metabat:
 
 rule maxbin:
     input:
-        fasta=BINNING_CONTIGS,
+        fasta=get_assembly,
         abund="{sample}/binning/coverage/{sample}_coverage.txt",
     output:
         directory("{sample}/binning/maxbin/intermediate_files"),
@@ -307,7 +305,7 @@ rule get_maxbin_cluster_attribution:
 rule get_bins:
     input:
         cluster_attribution="{sample}/binning/{binner}/cluster_attribution.tsv",
-        contigs=BINNING_CONTIGS,
+        contigs=get_assembly,
     output:
         directory("{sample}/binning/{binner}/bins"),
     conda:
@@ -337,7 +335,7 @@ rule run_das_tool:
             "{{sample}}/binning/DASTool/{binner}.scaffolds2bin",
             binner=config["binner"],
         ),
-        contigs=BINNING_CONTIGS,
+        contigs=get_assembly,
         proteins="{sample}/annotation/predicted_genes/{sample}.faa",
     output:
         "{sample}/binning/DASTool/{sample}_DASTool_summary.tsv",

diff --git a/workflow/rules/cobinning.smk b/workflow/rules/cobinning.smk
@@ -8,7 +8,7 @@ localrules:
 
 rule filter_contigs:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
     output:
         temp("Cobinning/filtered_contigs/{sample}.fasta"),
     params:
@@ -36,7 +36,7 @@ localrules:
 rule combine_contigs:
     input:
         #Trigers rerun if contigs change
-        flag=expand("{sample}/{sample}_contigs.fasta", sample=SAMPLES),
+        flag=expand("{sample}/{sample}_contigs.fasta", sample=SAMPLES), #TODO: this shoule be adapted using function get_assemblies
         fasta=ancient(expand(rules.filter_contigs.output[0], sample=SAMPLES)),
     output:
         "Cobinning/combined_contigs.fasta.gz",

diff --git a/workflow/rules/sample_table.smk b/workflow/rules/sample_table.smk
@@ -182,4 +182,17 @@ def get_quality_controlled_reads(wildcards, include_se=False):
 
 
 def get_assembly(wildcards):
-    return "{sample}/assembly/{sample}_contigs.fasta".format(sample=wildcards.sample )
+    """
+    Returns Assembly file for a given sample.
+
+    """
+
+    Header= "Assembly"
+    try:
+        return get_files_from_sampleTable(wildcards.sample, Header)
+
+    except FileNotInSampleTableException:
+        # return files as named by atlas pipeline
+
+        return "{sample}/assembly/{sample}_contigs.fasta".format(sample=wildcards.sample )
+
diff --git a/workflow/rules/semibin.smk b/workflow/rules/semibin.smk
@@ -34,7 +34,7 @@ rule semibin_generate_data_multi:
 
 rule semibin_train:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
         fasta=rules.filter_contigs.output,
         bams=expand(rules.sort_bam.output, sample=SAMPLES),
         data="Cobinning/SemiBin/samples/{sample}/data.csv",
@@ -66,7 +66,7 @@ rule semibin_train:
 
 rule run_semibin:
     input:
-        "{sample}/{sample}_contigs.fasta",
+        get_assembly,
         fasta=rules.filter_contigs.output,
         bams=expand(rules.sort_bam.output, sample=SAMPLES),
         data="Cobinning/SemiBin/samples/{sample}/data.csv",