refactor: add onstart directive in Snakefile (#57)

zavolanlab · Aug 14, 2021 · 5e50c5c · 5e50c5c
1 parent c76c6f0
commit 5e50c5c
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Showing 3 changed files with 10 additions and 58 deletions.
diff --git a/envs/dev.yml b/envs/dev.yml
@@ -34,5 +34,5 @@
     - shellcheck=0.7.0
     - snakemake=5.24.2
     - unzip=6.0
-  
+
 ...
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -32,6 +32,11 @@ def gather_motifs_names(pwm_dir):
     l = [i.split("/")[-1] for i in glob.glob(regex)]
     return(l)
 
+onstart:
+    shell("mkdir -p " + config["outdir"])
+    shell("mkdir -p " + config["outdir"] + "/local_log")
+    shell("mkdir -p " + config["outdir"] + "/cluster_log")
+
 rule all:
     """
     Target rule with final output of the pipeline
@@ -45,43 +50,6 @@ rule all:
             outdir = config["outdir"]
         )
 
-rule create_results_directory:
-    """
-    Create directories for the results
-    """
-    output:
-        TEMP_ = temp(
-            os.path.join(
-                "{outdir}",
-                "outdir"
-            )
-        )
-
-    params:
-        DIR_output_dir = "{outdir}",
-        LOG_local_log = os.path.join(
-            "{outdir}",
-            "local_log"
-        ),
-        LOG_cluster_log = os.path.join(
-            "{outdir}",
-            "cluster_log"
-        )
-
-    conda:
-        "envs/bash.yml"
-
-    singularity:
-        "docker://bash:4.4.18"   
-
-    shell:
-        """
-        mkdir -p {params.DIR_output_dir}; \
-        mkdir -p {params.LOG_local_log}; \
-        mkdir -p {params.LOG_cluster_log}; \
-        touch {output.TEMP_}
-        """
-
 rule plot_sequence_logos:
     """
     Plot sequence logo for the motifs
@@ -98,10 +66,6 @@ rule plot_sequence_logos:
             "workflow",
             "scripts",
             "sequence_logos.py"
-        ),
-        TEMP_ = os.path.join(
-            "{outdir}",
-            "outdir"
         )
 
     output:
@@ -159,12 +123,6 @@ rule prepare_MotEvo_parameters:
     """
     Prepare text file with parameters for MotEvo runs
     """
-    input:
-        TEMP_ = os.path.join(
-            "{outdir}",
-            "outdir"
-        )
-
     output:
         TXT_MotEvo_parameters = os.path.join(
             "{outdir}",
@@ -248,12 +206,6 @@ rule prepare_sequence_for_MotEvo:
     """
     Create a FASTA-formatted file with the input sequence
     """
-    input:
-        TEMP_ = os.path.join(
-            "{outdir}",
-            "outdir"
-        )
-
     output:
         FASTA_MotEvo_input = os.path.join(
             "{outdir}",

diff --git a/workflow/scripts/heatmap.r b/workflow/scripts/heatmap.r
@@ -21,25 +21,25 @@ library(ggtext)
 
 # list the command-line arguments
 option_list <- list(
-  make_option(c("--input_tsv"),
+  make_option("--input_tsv",
     action = "store",
     dest = "input_tsv",
     type = "character",
     help = "location and name of the tsv file"
   ),
-  make_option(c("--input_sequence"),
+  make_option("--input_sequence",
     action = "store",
     dest = "input_sequence",
     type = "character",
     help = "full input_sequence"
   ),
-  make_option(c("--outfile"),
+  make_option("--outfile",
     action = "store",
     dest = "output_tsv",
     type = "character",
     help = "location and name of output heatmap"
   ),
-  make_option(c("--sequence_logos_directory"),
+  make_option("--sequence_logos_directory",
     action = "store",
     dest = "sequence_logos_directory",
     type = "character",