Add rule to run salmon in SE mode

Add rule to run salmon in SE mode

added Doing label

assigned to @katsanto

################################################################################
### Salmon quantify based on reads
################################################################################

rule salmon_quant_reads:
    input:
        reads = os.path.join(config["output_dir"], "{sample}", "cutadapt", "trim_3p_adapter.fastq.gz"),
        index = os.path.join(config["output_dir"], "annotation", "annotation.filtered.canonical_and_transposon_transcripts.salmon.idx"),
        gtf = os.path.join(config["output_dir"], "annotation", "annotation.filtered.canonical_and_transposon_transcripts.transcriptid2geneid.txt")
    output:
        salmon_out = os.path.join(config["output_dir"], "{sample}", "salmon", "quant_reads", "quant.sf"),
        salmon_genes_out = os.path.join(config["output_dir"], "{sample}", "salmon", "quant_reads", "quant.genes.sf"),
    params:
        libType = "A",
        salmon_dir = os.path.join(config["output_dir"], "{sample}", "salmon", "quant_reads")
    log:
        os.path.join(config["local_log"], "salmon_quant_reads_{sample}.log")
    threads:    12
    conda:
        "envs/salmon.yaml"
    shell:
        "(salmon quant \
        --libType {params.libType} \
        --seqBias \
        --validateMappings \
        --threads {threads} \
        --writeUnmappedNames \
        --index {input.index} \
        --geneMap {input.gtf} \
        --unmatedReads {input.reads} \
        -o {params.salmon_dir}) &> {log}"

assigned to @devagy74 and unassigned @katsanto

rule create_index_salmon: input: transcriptome = sample_table.loc[wildcards.sample, 'filtered_fasta'] output: index = os.path.join( config["salmon_indexes"], sample_table["{sample}", 'organism'], "salmon.idx") params: kmerLen = lambda wildcards: sample_table.loc[wildcards.sample, 'kmer'] singularity: "docker://zavolab/salmon:0.11.0" log: os.path.join(config["local_log"], "paired_end", "{sample}", "create_index_salmon.log") threads: 8 shell: "(salmon index
--t {input.transcriptome}
--i {output.index}
--k {params.kmerLen}
--threads {threads}) &> {log}"

mentioned in merge request !4 (merged)

mentioned in commit 9017c055

closed via merge request !4 (merged)

removed Doing label

added 1 deleted label

mentioned in issue #48 (closed)

mentioned in merge request !15 (merged)

mentioned in commit ca9a2bb4