fix #4 + final workflow

project/config/config.yaml

@@ -2,10 +2,10 @@
 samples: "resources/sample/sample.tsv"
 human_reference: "resources/reference/human.fa"
 index: "results/reference/index"
-bowtieparams: "-q"
+bowtie_params: "-q"
 kraken_db: "/buffer/ag_bsc/pmsb_workflows_2022/kraken_standard_db/standard_db"
 viral_reference_alignment: "resources/reference/SARS-CoV-2.fasta"
 shiver_config_file: "config/shiver_config.sh"
 viral_sequencing_adapters: "resources/adapters/SARS-CoV-2.fasta"
 viral_sequencing_primers: "resources/primers/SARS-CoV-2.fasta"
-fastp_params: "--adapter_sequence TCTCGGTC --adapter_sequence_r2 GCGGACTT"
\ No newline at end of file
+fastp_params: "--adapter_sequence TCTCGGTC --adapter_sequence_r2 GCGGACTT"

project/workflow/rules/IVA.smk

 rule IVA:
+    message: 
+        "Genome Assembly..."
     input:
         fq1="results/unmapped_fastq/{sample}_1_unmapped.fastq",
         fq2="results/unmapped_fastq/{sample}_2_unmapped.fastq"
     output:
-        directory("results/IVA/{sample}/")
+        IVA_dir=directory("results/IVA/{sample}/")
     log:
         "logs/IVA/{sample}.log"
     threads: 16
     conda:
        "../envs/yourenv.yaml"
     shell:
-        "iva -f {input.fq1} -r {input.fq2} {output} --threads {threads} 2> {log}"
+        "iva -f {input.fq1} -r {input.fq2} {output.IVA_dir} --threads {threads} 2> {log}"
         
     
\ No newline at end of file

project/workflow/rules/bowtie2.smk

 rule refindex:
+    message:
+        "Building mapping index..."
     input:
         prefix=config["human_reference"]
     params:
         prefix=config["index"]
     output:
-        "results/reference/index.1.bt2"
+        "results/reference/index.bt2" 
     log:
         "logs/bowtie2/refindex/index.1.log"
     threads:4
     conda:
         "../envs/yourenv.yaml"
     shell:
-        "v1.3.2/bio/bowtie2/build"
+        "bowtie2-build {input} {params.prefix} > {output}"
 
 
 rule map:
+    message:
+        "Mapping reads to human reference..."
     input:
         idx=multiext(
             "results/reference/index",
@@ -27,7 +31,7 @@ rule map:
         ),
         sample=["results/fastp/trimmed/{sample}.1.fastq", "results/fastp/trimmed/{sample}.2.fastq"]
     params:
-        extra=config["bowtieparams"]
+        extra=config["bowtie_params"]
     output:
         "results/bam/{sample}.bam"
     threads:4

project/workflow/rules/fastp.smk

 rule fastp:
+    message: 
+        "Quality controlling raw data..."
     input:
         sample=["Data/SARS-Cov-2/{sample}_1.fastq.gz", "Data/SARS-Cov-2/{sample}_2.fastq.gz"]
     output:
         trimmed=["results/fastp/trimmed/{sample}.1.fastq", "results/fastp/trimmed/{sample}.2.fastq"],
-        html="report/fastp/{sample}.html",
-        json="report/fastp/{sample}.json"
+        html="results/fastp/report/{sample}.html",
+        json="results/fastp/report/{sample}.json"
     log:
         "logs/fastp/{sample}.log"
     conda:
         "../envs/yourenv.yaml"
     params:
-        extra=config["fastp_params]
+        extra=config["fastp_params"]
     threads: 4
     wrapper:
         "v1.3.2/bio/fastp"
\ No newline at end of file

project/workflow/rules/fastqc.smk

+rule rawfastqc1:
+  input:
+      rf1 = "Data/SARS-Cov-2/{sample}_1.fastq.gz"
+  output:
+      html="results/fastqc/raw/{sample}_1_fastqc.html",
+      zip="results/fastqc/raw/{sample}_1_fastqc.zip"
+  conda:
+      "../envs/yourenv.yaml"
+  log:
+      "logs/fastqc/{sample}.log"
+  wrapper:
+      "v1.3.1/bio/fastqc"
+
+
+rule rawfastqc2:
+  input:
+      rf2 = "Data/SARS-Cov-2/{sample}_2.fastq.gz"
+  output:
+      html="results/fastqc/raw/{sample}_2_fastqc.html",
+      zip="results/fastqc/raw/{sample}_2_fastqc.zip"
+  conda:
+      "../envs/yourenv.yaml"
+  log:
+      "logs/fastqc/{sample}.log"
+  wrapper:
+      "v1.3.1/bio/fastqc"
+
+
+rule trimmedfastqc1:
+    input:
+        sample=["results/fastp/trimmed/{sample}.1.fastq","results/fastp/trimmed/{sample}.2.fastq"]
+    output:
+        html="results/fastqc/trimmed/{sample}_1_fastqc.html",
+        zip="results/fastqc/trimmed/{sample}_1_fastqc.zip"
+    conda:
+        "../envs/yourenv.yaml"
+    log:
+        "logs/fastqc/trimmed_{sample}.log"
+    wrapper:
+        "v1.3.1/bio/fastqc"
+
+
+rule trimmedfastqc2:
+    input:
+        sample=["results/fastp/trimmed/{sample}.1.fastq","results/fastp/trimmed/{sample}.2.fastq"]
+    output:
+        html="results/fastqc/trimmed/{sample}_2_fastqc.html",
+        zip="results/fastqc/trimmed/{sample}_2_fastqc.zip"
+    conda:
+        "../envs/yourenv.yaml"
+    log:
+        "logs/fastqc/trimmed_{sample}.log"
+    wrapper:
+        "v1.3.1/bio/fastqc"

project/workflow/rules/kraken.smk

 rule build:
+    message:
+        "Building Kraken database..."
     output:
-        "krakendb"
+        database="krakendb"
     threads: 64
     conda:
         "../envs/yourenv.yaml"
@@ -18,8 +20,10 @@ rule build:
         """ 
 
 rule report_trimmedreads:
+    message:
+        "Creating Kraken report using trimmed reads..."
     input:
-        db=config["kraken_db"],
+        database=config["kraken_db"],
         sample=["results/fastp/trimmed/{sample}.1.fastq", "results/fastp/trimmed/{sample}.2.fastq"]
     output:
         output="results/kraken/{sample}_trimmed.kraken",
@@ -30,11 +34,13 @@ rule report_trimmedreads:
     log:
         "logs/kraken/report/{sample}_trimmed.log"
     shell:
-        "kraken2 --threads {threads} --db {input.db} --paired {input.sample} --report {output.report} > {output.output} 2> {log}"
+        "kraken2 --threads {threads} --db {input.database} --paired {input.sample} --report {output.report} > {output.output} 2> {log}"
 
 rule report_unmappedreads:
+    message: 
+        "Creating Kraken report using unmapped reads..."
     input:
-        db="/buffer/ag_bsc/pmsb_workflows_2022/kraken_standard_db/standard_db",
+        database="/buffer/ag_bsc/pmsb_workflows_2022/kraken_standard_db/standard_db",
         sample=["results/unmapped_fastq/{sample}_1_unmapped.fastq", "results/unmapped_fastq/{sample}_2_unmapped.fastq"]
     output:
         output="results/kraken/{sample}_unmapped.kraken",
@@ -45,4 +51,4 @@ rule report_unmappedreads:
     log:
         "logs/kraken/report/{sample}_unmapped.log"
     shell:
-        "kraken2 --threads {threads} --db {input.db} --paired {input.sample} --report {output.report} > {output.output} 2> {log}"
\ No newline at end of file
+        "kraken2 --threads {threads} --db {input.database} --paired {input.sample} --report {output.report} > {output.output} 2> {log}"
\ No newline at end of file

project/workflow/rules/multiqc.smk

 rule multiqc:
+    message:
+        "Creating MultiQC report..."
     input:
-        "results/"
+        results="results/",
+        fastp="results/fastp/report/"
     output:
-        "results/multiqc/multiqc.html"
+        report="results/multiqc/multiqc.html"
     conda:
         "../envs/yourenv.yaml"
     shell:
         """
-        multiqc -n multiqc.html {input}
-        mv multiqc.html {output}
+        multiqc -n multiqc.html {input.results} {input.fastp} 
+        mv multiqc.html {output.report}
+        mv multiqc_data/ results/
         """
\ No newline at end of file

project/workflow/rules/quast.smk

 rule quast_IVA:
+    message:
+        "Creating QUAST report for IVA contigs..."
     input:
-        "results/IVA/{sample}/contigs.fasta"
+        contigs="results/IVA/{sample}/contigs.fasta"
     output:
-        directory("results/quast_IVA/{sample}")
+        quast_dir=directory("results/quast_IVA/{sample}")
     conda:
         "../envs/quast.yaml"
     threads: 4
     log:
         "logs/quast_IVA/{sample}.log"
     shell:
-        "quast -o {output} -t {threads} {input} 2> {log}"
+        "quast -o {output.quast_dir} -t {threads} {input.contigs} 2> {log}"
 
 
 rule quast_shiver:
+    message:
+        "Creating QUAST report for shiver consensus genome..."
     input:
         consensus_genome="results/shiver/{sample}/{sample}.fasta",
         quast_ref_genome=config["viral_reference_alignment"]

project/workflow/rules/samtools.smk

 rule fastq:
+    message:
+        "Extracting unmapped reads..."
     input:
-        "results/bam/{sample}.bam"
+        bam="results/bam/{sample}.bam"
     output:
         fq1="results/unmapped_fastq/{sample}_1_unmapped.fastq",
         fq2="results/unmapped_fastq/{sample}_2_unmapped.fastq"
@@ -11,7 +13,7 @@ rule fastq:
        "../envs/yourenv.yaml"
     shell:
         """
-        samtools view --threads={threads} -b -f4 {input} > results/bam/{wildcards.sample}_unmapped.bam 2> {log} 
+        samtools view --threads={threads} -b -f4 {input.bam} > results/bam/{wildcards.sample}_unmapped.bam 2> {log} 
         samtools sort -n results/bam/{wildcards.sample}_unmapped.bam -o results/bam/{wildcards.sample}_sorted.bam 2>> {log}
         bedtools bamtofastq -i results/bam/{wildcards.sample}_sorted.bam -fq {output.fq1} -fq2 {output.fq2} 2>> {log}
         """

project/workflow/rules/shiver.smk

 rule shiver_initialization:
+    message: 
+        "Initializing shiver..."
     input:
         reference_alignment=config["viral_reference_alignment"],
         adapters=config["viral_sequencing_adapters"],
         primers=config["viral_sequencing_primers"],
         shiver_config=config["shiver_config_file"]
     output:
-        initialization_directory=directory("results/shiver/{sample}/{sample}_shiver_init_dir")
+        initialization_dir=directory("results/shiver/{sample}/{sample}_shiver_init_dir")
     conda:
         "../envs/shiver.yaml"
     log:
         "logs/shiver/{sample}/{sample}_init.log"   
     shell:
-        "shiver_init.sh {output.initialization_directory} {input.shiver_config} {input.reference_alignment} {input.adapters} {input.primers} 2> {log}"
+        "shiver_init.sh {output.initialization_dir} {input.shiver_config} {input.reference_alignment} {input.adapters} {input.primers} 2> {log}"
 
 
 rule shiver_align_contigs_to_reference:
+    message:
+        "Aligning contigs to reference..."
     input:
-        initialization_directory=rules.shiver_initialization.output.initialization_directory,
+        initialization_dir=rules.shiver_initialization.output.initialization_dir,
         contigs_file="results/IVA/{sample}/contigs.fasta",
         shiver_config=config["shiver_config_file"]
     output:
@@ -31,15 +35,17 @@ rule shiver_align_contigs_to_reference:
         """
         mkdir shiver_temp_{wildcards.sample}
         cd shiver_temp_{wildcards.sample}
-        shiver_align_contigs.sh ../{input.initialization_directory} ../{input.shiver_config} ../{input.contigs_file} ../results/shiver/{wildcards.sample}/{wildcards.sample} > ../{log} 2>&1
+        shiver_align_contigs.sh ../{input.initialization_dir} ../{input.shiver_config} ../{input.contigs_file} ../results/shiver/{wildcards.sample}/{wildcards.sample} > ../{log} 2>&1
         cd ..
         rm -r shiver_temp_{wildcards.sample}
         """
 
 
 rule shiver_read_remapping:
+    message:
+        "Mapping..."
     input:
-        initialization_directory=rules.shiver_initialization.output.initialization_directory,
+        initialization_dir=rules.shiver_initialization.output.initialization_dir,
         contigs="results/IVA/{sample}/contigs.fasta",
         aligned_contigs_raw=rules.shiver_align_contigs_to_reference.output.aligned_contigs_raw,
         blast_hits=rules.shiver_align_contigs_to_reference.output.blast_hits,
@@ -63,16 +69,18 @@ rule shiver_read_remapping:
         """
         mkdir shiver_temp_{wildcards.sample}
         cd shiver_temp_{wildcards.sample}
-        shiver_map_reads.sh ../{input.initialization_directory} ../{input.shiver_config} ../{input.contigs} ../results/shiver/{wildcards.sample}/{wildcards.sample} ../{input.blast_hits} ../{input.aligned_contigs_raw} ../{input.forward_read} ../{input.reverse_read} > ../{log} 2>&1
+        shiver_map_reads.sh ../{input.initialization_dir} ../{input.shiver_config} ../{input.contigs} ../results/shiver/{wildcards.sample}/{wildcards.sample} ../{input.blast_hits} ../{input.aligned_contigs_raw} ../{input.forward_read} ../{input.reverse_read} > ../{log} 2>&1
         cd ..
         rm -r shiver_temp_{wildcards.sample}
         """
 
 rule tidy_shiver_output:
+    message:
+        "Tidying up..."
     input:
         consensus_genome="results/shiver/{sample}/{sample}_remap_consensus_MinCov_15_30.fasta"
     output:
-        "results/shiver/{sample}/{sample}.fasta"
+        tidy_consensus_genome="results/shiver/{sample}/{sample}.fasta"
     conda:
         "../envs/shiver.yaml"
     log:

project/workflow/snakefile

@@ -3,27 +3,31 @@ configfile: "config/config.yaml"
 
 samples = pd.read_table(config["samples"], index_col="sample")
 
+
 rule all:
     input:
-        #"krakendb"
-        #"results/kraken/ERR4181713_report.txt"
-        #expand("results/kraken/{sample}_trimmed.kraken", sample=samples.index)
+        "results/multiqc/multiqc.html",
         #expand("results/fastp/trimmed/{sample}.1.fastq", sample=samples.index),
-        #expand("results/fastp/trimmed/{sample}.2.fastq", sample=samples.index),
-        #expand("results/IVA/{sample}", sample=samples.index)
+        expand("results/fastp/report/{sample}.json", sample=samples.index),
+        #expand("results/fastqc/raw/{sample}_1_fastqc.html", sample=samples.index),
+        #expand("results/fastqc/raw/{sample}_2_fastqc.html", sample=samples.index),
+        #expand("results/fastqc/trimmed/{sample}_1_fastqc.html", sample=samples.index),
+        #expand("results/fastqc/trimmed/{sample}_2_fastqc.html", sample=samples.index),
+
+        #"results/reference/index.bt2",
+
         #expand("results/kraken/{sample}_trimmed.kraken", sample=samples.index),
         #expand("results/kraken/{sample}_trimmed.kreport2", sample=samples.index),
         #expand("results/kraken/{sample}_unmapped.kraken", sample=samples.index),
-        #expand("results/kraken/{sample}_unmapped.kreport2", sample=samples.index)
-        #expand("results/shiver/{sample}/{sample}_shiver_init_dir", sample=samples.index)
-        #expand("results/shiver/{sample}/{sample}_remap_consensus_MinCov_15_30.fasta", sample=samples.index)
-        #expand("results/fastqc/raw/{sample}_1_fastqc.html", sample=samples.index),
-        #expand("results/fastqc/raw/{sample}_2_fastqc.html", sample=samples.index),
-        #expand("results/trimmed_fastqc/{sample}_1_fastqc.html", sample=samples.index),
-        #expand("results/trimmed_fastqc/{sample}_2_fastqc.html", sample=samples.index)
-        #expand("results/shiver/{sample}/{sample}.fasta", sample=samples.index)
-        #expand("results/quast_shiver/{sample}", sample=samples.index)
-        "results/multiqc/multiqc.html"
+        #expand("results/kraken/{sample}_unmapped.kreport2", sample=samples.index),
+        
+        #expand("results/IVA/{sample}", sample=samples.index),
+        #expand("results/shiver/{sample}/{sample}_shiver_init_dir", sample=samples.index),
+        #expand("results/shiver/{sample}/{sample}_remap_consensus_MinCov_15_30.fasta", sample=samples.index),
+        
+        #expand("results/shiver/{sample}/{sample}.fasta", sample=samples.index),
+        #expand("results/quast_shiver/{sample}", sample=samples.index),
+        
 
 include: "rules/fastp.smk"
 include: "rules/bowtie2.smk"
@@ -37,3 +41,4 @@ include: "rules/multiqc.smk"
 
 
 
+