fix: chip input issue

README.md

@@ -4,4 +4,4 @@
 
 Pipeline based on snakemake to process ChIP-seq, ATAC-seq, RNA-seq and short read WGS data for SNP calling.
 
-See the [SeqNado documentation](alsmith151.github.io/SeqNado/) for more information.
+See the SeqNado documentation https://alsmith151.github.io/SeqNado/ for more information. 

docs/faq.md

@@ -5,3 +5,17 @@
 ### Workflow defines configfile config_chip.yml but it is not present or accessible.
 
 This error occurs when the pipeline is run without a config file present in the working directory. Follow the [Pipeline Setup](pipeline.md#create-a-design-file) instructions to create a config file.
+
+
+## Singularity configuration
+
+### Workflow Error
+
+Failed to pull singularity image from library://asmith151/seqnado/seqnado_pipeline:latest:  
+FATAL: Unable to get library client configuration:  
+remote has no library client (see https://apptainer.org/docs/user/latest/endpoint.html#no-default-remote)
+
+Fix:
+
+apptainer remote add --no-login SylabsCloud cloud.sylabs.io  
+apptainer remote use SylabsCloud  

docs/pipeline.md

@@ -10,6 +10,11 @@ The following command will generate the working directory and configuration file
 
 ```bash
 seqnado-config chip
+
+# options 
+-r, --rerun # Re-run the config
+-g, --genome [dm6|hg19|hg38|hg38_dm6|hg38_mm39|hg38_spikein|mm10|mm39|other] # Genome to use if genome preset is configured
+
 ```
 
 You should get somthing like this:

seqnado/cli.py

@@ -9,6 +9,7 @@
 
 @click.command(context_settings=dict(ignore_unknown_options=True))
 @click.argument("method", type=click.Choice(["atac", "chip", "rna", "snp"]))
+@click.option("-r", "--rerun", is_flag=True, help="Re-run the config")
 @click.option(
     "-g",
     "--genome",
@@ -28,13 +29,13 @@
         ]
     ),
 )
-def cli_config(method, help=False, genome="other"):
+def cli_config(method, help=False, genome="other", rerun=False):
     """
     Runs the config for the data processing pipeline.
     """
     import seqnado.config as config
 
-    config.create_config(method, genome)
+    config.create_config(method, genome, rerun)
 
 
 @click.command()

seqnado/config.py

@@ -178,7 +178,7 @@ def setup_configuration(assay, genome, template_data):
     colormap: RdYlBu_r
 """
 
-def create_config(assay, genome):
+def create_config(assay, genome, rerun):
     env = Environment(loader=FileSystemLoader(template_dir), auto_reload=False)
 
     template = env.get_template("config.yaml.jinja")        
@@ -189,15 +189,20 @@ def create_config(assay, genome):
 
     # Setup configuration
     setup_configuration(assay, genome, template_data)
-
-    # Create directory and render template
-    dir_name = f"{template_data['project_date']}_{template_data['assay']}_{template_data['project_name']}"
-    os.makedirs(dir_name, exist_ok=True)
-    fastq_dir = os.path.join(dir_name, "fastq")
-    os.makedirs(fastq_dir, exist_ok=True)
 
-    with open(os.path.join(dir_name, f"config_{assay}.yml"), 'w') as file:
-        file.write(template.render(template_data))
+    # Create directory and render template
+    if rerun:
+        dir_name = os.getcwd()
+        with open(os.path.join(dir_name, f"config_{assay}.yml"), 'w') as file:
+            file.write(template.render(template_data))
+    else:
+        dir_name = f"{template_data['project_date']}_{template_data['assay']}_{template_data['project_name']}"
+        os.makedirs(dir_name, exist_ok=True)
+        fastq_dir = os.path.join(dir_name, "fastq")
+        os.makedirs(fastq_dir, exist_ok=True)
+
+        with open(os.path.join(dir_name, f"config_{assay}.yml"), 'w') as file:
+            file.write(template.render(template_data))
 
     # add deseq2 qmd file if rna
     if assay == "rna":

seqnado/utils.py

@@ -624,6 +624,7 @@ def to_dataframe(self, simplify: bool = True):
 
     @classmethod
     def from_dataframe(cls, df: pd.DataFrame, simplified: bool = True, **kwargs):
+
         experiments = {}
         for experiment_name, row in df.iterrows():
             if simplified:
@@ -682,71 +683,45 @@ def from_dataframe(cls, df: pd.DataFrame, simplified: bool = True, **kwargs):
 
         return cls(assays=experiments, **kwargs)
 
-
-def symlink_files_paired(
-    output_dir: pathlib.Path, assay: Union[AssayNonIP, AssayIP], assay_name: str
-):
-    r1_path_new = pathlib.Path(f"{output_dir}/{assay_name}_1.fastq.gz")
-    r2_path_new = pathlib.Path(f"{output_dir}/{assay_name}_2.fastq.gz")
-
-    if not r1_path_new.exists():
-        try:
-            r1_path_new.symlink_to(assay.r1.path.resolve())
-        except FileExistsError:
-            logger.warning(f"Symlink for {r1_path_new} already exists.")
-
-    if assay.r2 and not r2_path_new.exists():
-        try:
-            r2_path_new.symlink_to(assay.r2.path.resolve())
-        except FileExistsError:
-            logger.warning(f"Symlink for {r2_path_new} already exists.")
-
-
-def symlink_files_single(
-    output_dir: pathlib.Path, assay: Union[AssayNonIP, AssayIP], assay_name: str
-):
-    r1_path_new = pathlib.Path(f"{output_dir}/{assay_name}.fastq.gz")
-
-    if not r1_path_new.exists():
+def symlink_file(output_dir: pathlib.Path, source_path: pathlib.Path, new_file_name: str):
+    """
+    Create a symlink in the output directory with the new file name.
+    """
+    new_path = output_dir / new_file_name
+    if not new_path.exists():
         try:
-            r1_path_new.symlink_to(assay.r1.path.resolve())
+            new_path.symlink_to(source_path.resolve())
         except FileExistsError:
-            logger.warning(f"Symlink for {r1_path_new} already exists.")
+            logger.warning(f"Symlink for {new_path} already exists.")
 
-
-def symlink_fastq_files(
-    design: Union[Design, DesignIP], output_dir: str = "seqnado_output/fastqs/"
-) -> None:
+def symlink_fastq_files(design: Union[Design, DesignIP], output_dir: str = "seqnado_output/fastqs/") -> None:
     """
     Symlink the fastq files to the output directory.
     """
     output_dir = pathlib.Path(output_dir)
     output_dir.mkdir(parents=True, exist_ok=True)
-
+    
     if isinstance(design, Design):
         for assay_name, assay in design.assays.items():
+            symlink_file(output_dir, assay.r1.path, f"{assay_name}_1.fastq.gz")
             if assay.is_paired:
-                symlink_files_paired(output_dir, assay, assay_name)
-            else:
-                symlink_files_single(output_dir, assay, assay_name)
+                symlink_file(output_dir, assay.r2.path, f"{assay_name}_2.fastq.gz")
 
     elif isinstance(design, DesignIP):
         for experiment_name, experiment in design.assays.items():
-            assay = experiment.ip_files
-            assay_name = assay.name
-
-            if assay.is_paired:
-                symlink_files_paired(output_dir, assay, assay_name)
-            else:
-                symlink_files_single(output_dir, assay, assay_name)
+            # IP files
+            ip_assay = experiment.ip_files
+            symlink_file(output_dir, ip_assay.r1.path, f"{ip_assay.name}_1.fastq.gz")
+            if ip_assay.is_paired:
+                symlink_file(output_dir, ip_assay.r2.path, f"{ip_assay.name}_2.fastq.gz")
 
             if experiment.control_files:
-                assay = experiment.control_files
-                assay_name = assay.name
-                if assay.is_paired:
-                    symlink_files_paired(output_dir, assay, assay_name)
-                else:
-                    symlink_files_single(output_dir, assay, assay_name)
+                control_assay = experiment.control_files
+                control_r1_name = control_assay.r1.path.name 
+                symlink_file(output_dir, control_assay.r1.path, control_r1_name)
+                if control_assay.is_paired:
+                    control_r2_name = control_assay.r2.path.name 
+                    symlink_file(output_dir, control_assay.r2.path, control_r2_name)
 
 
 def define_output_files(

seqnado/workflow/rules/hub.smk

@@ -93,6 +93,30 @@ def get_hub_input(wildcards):
     return input_files
 
 
+def get_peak_files(wildcards):
+    peak_files = []
+
+    if config["call_peaks"]:
+        if ASSAY == "ChIP":
+            peak_files.extend(
+                expand(
+                    "seqnado_output/peaks/{method}/{sample}.bed",
+                    method=config["peak_calling_method"],
+                    sample=SAMPLE_NAMES_IP,
+                )
+            )
+        elif ASSAY == "ATAC":
+            peak_files.extend(
+                expand(
+                    "seqnado_output/peaks/{method}/{sample}.bed",
+                    method=config["peak_calling_method"],
+                    sample=SAMPLE_NAMES,
+                )
+            )
+
+    return peak_files
+
+
 rule save_design:
     output:
         "seqnado_output/design.csv",
@@ -102,9 +126,33 @@ rule save_design:
         DESIGN.to_dataframe().to_csv("seqnado_output/design.csv", index=False)
 
 
+rule validate_peaks:
+    input:
+        peaks=get_peak_files,
+    output:
+        sentinel="seqnado_output/peaks/.validated",
+    container:
+        None
+    log:
+        "seqnado_output/logs/validate_peaks.log",
+    run:
+        from loguru import logger
+
+        with logger.catch():
+            for peak_file in input.peaks:
+                with open(peak_file, "r+") as p:
+                    peak_entries = p.readlines()
+                    if len(peak_entries) < 1:
+                        p.write("chr21\t1\t2\n")
+
+        with open(output.sentinel, "w") as s:
+            s.write("validated")
+
+
 rule bed_to_bigbed:
     input:
         bed="seqnado_output/peaks/{directory}/{sample}.bed",
+        sentinel="seqnado_output/peaks/.validated",
     output:
         bigbed="seqnado_output/peaks/{directory}/{sample}.bigBed",
     params:
@@ -149,3 +197,4 @@ rule generate_hub:
 
 localrules:
     generate_hub,
+    validate_peaks,

seqnado/workflow/rules/peak_call_chip.smk

@@ -12,17 +12,26 @@ def get_lanceotron_threshold(wildcards):
 
 def get_control_bam(wildcards):
     exp = DESIGN.query(sample_name=wildcards.sample, ip=wildcards.treatment)
-    return "seqnado_output/aligned/{sample}_{exp.control}.bam"
+    control = f"seqnado_output/aligned/{wildcards.sample}_{exp.control}.bam".replace(
+        " ", ""
+    )
+    return control
 
 
 def get_control_tag(wildcards):
     exp = DESIGN.query(sample_name=wildcards.sample, ip=wildcards.treatment)
-    return "seqnado_output/tag_dirs/{sample}_{exp.control}"
+    control = f"seqnado_output/tag_dirs/{wildcards.sample}_{exp.control}".replace(
+        " ", ""
+    )
+    return control
 
 
 def get_control_bigwig(wildcards):
     exp = DESIGN.query(sample_name=wildcards.sample, ip=wildcards.treatment)
-    return "seqnado_output/bigwigs/deeptools/{sample}_{exp.control}.bigWig"
+    control = f"seqnado_output/bigwigs/deeptools/{wildcards.sample}_{exp.control}.bigWig".replace(
+        " ", ""
+    )
+    return control
 
 
 rule macs2_with_input:
@@ -43,7 +52,7 @@ rule macs2_with_input:
     shell:
         """
         macs2 callpeak -t {input.treatment} -c {input.control} -n seqnado_output/peaks/macs/{wildcards.treatment} -f BAMPE {params.options} > {log} 2>&1 &&
-        cat {params.narrow} | cut -f 1-3 > {output.peaks}
+        cat {params.narrow} | cut -f 1-3 > {output.peaks} || touch {output.peaks}
         """
 
 
@@ -132,7 +141,7 @@ rule lanceotron_with_input:
     shell:
         """
         lanceotron callPeaksInput {input.treatment} -i {input.control} -f {params.outdir} --skipheader > {log} 2>&1 &&
-        cat {params.outdir}/{wildcards.treatment}_L-tron.bed | awk 'BEGIN{{OFS="\\t"}} $4 >= {params.threshold} {{print $1, $2, $3}}' > {output.peaks}
+        cat {params.outdir}/{wildcards.treatment}_L-tron.bed | awk 'BEGIN{{OFS="\\t"}} $4 >= {params.threshold} {{print $1, $2, $3}}' > {output.peaks} || touch {output.peaks}
         """
 
 
@@ -159,4 +168,6 @@ rule lanceotron_no_input:
         """
 
 
-ruleorder: lanceotron_with_input > lanceotron_no_input > homer_with_input > homer_no_input > macs2_with_input > macs2_no_input
+ruleorder: lanceotron_with_input > lanceotron_no_input
+ruleorder: homer_with_input > homer_no_input
+ruleorder: macs2_with_input > macs2_no_input