deseq and heatmap changes

alsmith151 · Jan 11, 2024 · e6f199c · e6f199c
1 parent 1286f4b
commit e6f199c
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Showing 8 changed files with 26 additions and 24 deletions.
diff --git a/seqnado/config.py b/seqnado/config.py
@@ -119,7 +119,6 @@ def setup_configuration(assay, genome, template_data):
     if template_data['split_fastq']:
         template_data.update['split_fastq_parts'] = get_user_input("How many parts do you want to split the FASTQ files into?", default="4")
 
-
     template_data['make_bigwigs'] = get_user_input("Do you want to make bigwigs? (yes/no)", default="no", is_boolean=True)
     if template_data['make_bigwigs']:
         template_data['pileup_method'] = get_user_input("Pileup method:", default="deeptools", choices=["deeptools", "homer"])
@@ -184,7 +183,7 @@ def setup_configuration(assay, genome, template_data):
     callpeak: -c 0.5
 
 heatmap:
-    options:
+    options: --binSize 100 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --regionBodyLength 5000
     colormap: RdYlBu_r
 """
 
@@ -215,7 +214,7 @@ def setup_configuration(assay, genome, template_data):
     bamcoverage: -bs 1 --normalizeUsing CPM
 
 heatmap:
-    options:
+    options: --binSize 100 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --regionBodyLength 5000
     colormap: RdYlBu_r
 """
 

diff --git a/seqnado/utils.py b/seqnado/utils.py
@@ -195,7 +195,7 @@ def fastq_files(self):
     @property
     def sample_names_all(self):
         return self.design["sample"].to_list()
-
+    
     @property
     def translation(self):
         fq_translation = {}
@@ -346,6 +346,16 @@ def define_output_files(
                 )
 
     elif assay == "RNA":
+        assay_output.extend(
+            [
+                "seqnado_output/feature_counts/read_counts.tsv",
+                *expand(
+                    "seqnado_output/aligned/{sample}.bam",
+                    sample=sample_names,
+                ),
+            ]
+        )
+
         if make_bigwigs and pileup_method:
             assay_output.extend(
                 expand(
@@ -357,18 +367,9 @@ def define_output_files(
             )
 
         if run_deseq2:
-            project_id = kwargs["deseq2"].get("project_id")
-            assay_output.append(f"DESeq2_{project_id}.html")
+            project_id = kwargs["project_name"]
+            assay_output.append(f"deseq2_{project_id}.html")
 
-        assay_output.extend(
-            [
-                "seqnado_output/feature_counts/read_counts.tsv",
-                *expand(
-                    "seqnado_output/aligned/{sample}.bam",
-                    sample=sample_names,
-                ),
-            ]
-        )
 
     elif assay == "SNP":
         if call_snps:

diff --git a/seqnado/workflow/rules/deseq2_rna.smk b/seqnado/workflow/rules/deseq2_rna.smk
@@ -3,9 +3,9 @@ if config["run_deseq2"]:
     rule deseq2_report_rnaseq:
         input:
             counts="seqnado_output/feature_counts/read_counts.tsv",
-            qmd=f"DESeq2_{config['project_name']}.qmd",
+            qmd=f"deseq2_{config['project_name']}.qmd",
         output:
-            deseq2=f"DESeq2_{config['project_name']}.html",
+            deseq2=f"deseq2_{config['project_name']}.html",
         log:
             "seqnado_output/logs/deseq2/deseq2.log",
         container:

diff --git a/seqnado/workflow/rules/heatmap.smk b/seqnado/workflow/rules/heatmap.smk
@@ -23,7 +23,7 @@ rule heatmap_matrix:
         mem_mb=lambda wildcards, attempt: 16000 * 2**attempt,
     log: 
         "seqnado_output/logs/heatmap/matrix.log",
-    shell: """computeMatrix scale-regions --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --regionBodyLength 5000 --smartLabels --missingDataAsZero -p {threads} {params.options} -S {input.bigwigs} -R {params.gtf} -o {output.matrix} >> {log} 2>&1"""
+    shell: """computeMatrix scale-regions -p {threads} {params.options} --smartLabels --missingDataAsZero -S {input.bigwigs} -R {params.gtf} -o {output.matrix} >> {log} 2>&1"""
 
 rule heatmap_plot:
     input:
@@ -44,8 +44,6 @@ rule heatmap_metaplot:
         matrix="seqnado_output/heatmap/heatmap_matrix.mat.gz",
     output:
         metaplot="seqnado_output/heatmap/metaplot.pdf",
-    params:
-        colormap = utils.check_options(config["heatmap"]["colormap"]),
     resources:
         mem_mb=lambda wildcards, attempt: 2000 * 2**attempt,
     log: 

diff --git a/seqnado/workflow/snakefile_atac b/seqnado/workflow/snakefile_atac
@@ -58,8 +58,9 @@ rule all:
 onsuccess:
     slurm_files = glob.glob("slurm-*.out")
     sps_files = glob.glob("sps-*")
+    simg_files = glob.glob("*.simg")
 
-    for fn in [*slurm_files, *sps_files]:
+    for fn in [*slurm_files, *sps_files, *simg_files]:
         try:
             if not os.path.isdir(fn):
                 os.remove(fn)

diff --git a/seqnado/workflow/snakefile_chip b/seqnado/workflow/snakefile_chip
@@ -73,8 +73,9 @@ rule all:
 onsuccess:
     slurm_files = glob.glob("slurm-*.out")
     sps_files = glob.glob("sps-*")
+    simg_files = glob.glob("*.simg")
 
-    for fn in [*slurm_files, *sps_files]:
+    for fn in [*slurm_files, *sps_files, *simg_files]:
         try:
             if not os.path.isdir(fn):
                 os.remove(fn)

diff --git a/seqnado/workflow/snakefile_rna b/seqnado/workflow/snakefile_rna
@@ -65,8 +65,9 @@ rule all:
 onsuccess:
     slurm_files = glob.glob("slurm-*.out")
     sps_files = glob.glob("sps-*")
+    simg_files = glob.glob("*.simg")
 
-    for fn in [*slurm_files, *sps_files]:
+    for fn in [*slurm_files, *sps_files, *simg_files]:
         try:
             if not os.path.isdir(fn):
                 os.remove(fn)

diff --git a/seqnado/workflow/snakefile_snp b/seqnado/workflow/snakefile_snp
@@ -56,8 +56,9 @@ rule all:
 onsuccess:
     slurm_files = glob.glob("slurm-*.out")
     sps_files = glob.glob("sps-*")
+    simg_files = glob.glob("*.simg")
 
-    for fn in [*slurm_files, *sps_files]:
+    for fn in [*slurm_files, *sps_files, *simg_files]:
         try:
             if not os.path.isdir(fn):
                 os.remove(fn)