SnakeMake workflow for the processing of RNAseq data

public public 1yr ago Version: v0.1 0 bookmarks
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smk_rnaseq
smk_rnaseq
smk_rnaseq
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shell:
	"""
	featureCounts -p -a {params.saf} -o {output.readcounts} -F SAF -t {input.bams}
	"""
SnakeMake FeatureCounts From line 21 of rules/featurecounts.smk 
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shell:
	"""
	bbmap.sh slow k=11 in={input.read1} in2={input.read2} ref={params.ref_genome} out={output.mapped} statsfile={output.mapping_stats}
	samtools sort {output.mapped} -o {output.mapped_sorted}
	samtools index {output.mapped_sorted}
	"""
SnakeMake SAMtools BBMap From line 24 of rules/mapping.smk 
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shell:
    """
    fastqc {input.read} -t {threads} -f fastq --outdir logs/fastqc/raw
    """
SnakeMake FastQC From line 22 of rules/qc.smk 
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	shell:
		"""
		bbduk.sh -Xmx8g in1={input.read1} in2={input.read2} out1={output.read1} out2={output.read2} stats={output.trim_stats} minlen=75 qtrim=rl trimq=20 ktrim=r k=25 mink=11 ref={params.adapter} hdist=1
        """
SnakeMake BBMap From line 40 of rules/qc.smk 
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shell:
    """
    fastqc {input.read} -t {threads} -f fastq --outdir logs/fastqc/trimmed
    """
SnakeMake FastQC From line 56 of rules/qc.smk 
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shell:
	"""
	merge-paired-reads.sh {input.read1} {input.read2} {params.merged}
	sortmerna --ref {params.ssu_bac_db},{params.ssu_bac_idx}:{params.lsu_bac_db},{params.lsu_bac_idx} --reads {params.merged} --other {params.merged_mRNA} --aligned {params.merged_rRNA} --fastx --best 5 --paired_in -a 4 -v --blast 1 --log 2> {log}
	unmerge-paired-reads.sh {params.merged_mRNA_fq} {output.read1} {output.read2}
	rm {params.merged}
	rm {params.merged_rRNA_fq}
	rm {params.merged_mRNA_fq}
	"""
SnakeMake From line 46 of rules/sortmerna.smk
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/wegnerce/smk_rnaseq
Name: smk_rnaseq
Version: v0.1
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Copyright: Public Domain
License: GNU General Public License v3.0
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